R-universe search: legend

bioc

ComplexHeatmap:Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing clustering complex-heatmaps heatmap

47.6 match 1.3k stars 16.93 score 16k scripts 151 dependents

stefanedwards

lemon:Freshing Up your 'ggplot2' Plots

Functions for working with legends and axis lines of 'ggplot2', facets that repeat axis lines on all panels, and some 'knitr' extensions.

Maintained by Stefan McKinnon Edwards. Last updated 4 months ago.

axis-lines facets ggplot-extension ggplot2 knitr legend ticks visualization

30.0 match 190 stars 11.98 score 1.7k scripts 4 dependents

riatelab

cartography:Thematic Cartography

Create and integrate maps in your R workflow. This package helps to design cartographic representations such as proportional symbols, choropleth, typology, flows or discontinuities maps. It also offers several features that improve the graphic presentation of maps, for instance, map palettes, layout elements (scale, north arrow, title...), labels or legends. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.

Maintained by Timothée Giraud. Last updated 2 years ago.

cartography map thematic-maps cpp

19.6 match 399 stars 10.47 score 460 scripts 2 dependents

teunbrand

legendry:Extended Legends and Axes for 'ggplot2'

A 'ggplot2' extension that focusses on expanding the plotter's arsenal of guides. Guides in 'ggplot2' include axes and legends. 'legendry' offers new axes and annotation options, as well as new legends and colour displays.

Maintained by Teun van den Brand. Last updated 11 days ago.

axis axis-customization ggplot-extension ggplot2 legend visualization

21.2 match 227 stars 7.83 score 29 scripts 2 dependents

tidyverse

ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics

A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.

Maintained by Thomas Lin Pedersen. Last updated 9 days ago.

data-visualisation visualisation

6.0 match 6.6k stars 25.10 score 645k scripts 7.5k dependents

dmurdoch

plotrix:Various Plotting Functions

Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.

Maintained by Duncan Murdoch. Last updated 1 years ago.

13.2 match 5 stars 11.31 score 9.2k scripts 361 dependents

liamrevell

phytools:Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Maintained by Liam J. Revell. Last updated 27 days ago.

10.1 match 218 stars 13.85 score 4.8k scripts 76 dependents

riatelab

maplegend:Legends for Maps

Create legends for maps and other graphics. Thematic maps need to be accompanied by legible legends to be fully comprehensible. This package offers a wide range of legends useful for cartography, some of which may also be useful for other types of graphics.

Maintained by Timothée Giraud. Last updated 5 months ago.

legend maps

21.5 match 13 stars 6.33 score 5 scripts 14 dependents

mkajano

HDXBoxeR:Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

A protocol that facilitates the processing and analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data using p-value statistics and Critical Interval analysis. It provides a pipeline for analyzing data from 'HDXExaminer' (Sierra Analytics, Trajan Scientific), automating matching and comparison of protein states through Welch's T-test and the Critical Interval statistical framework. Additionally, it simplifies data export, generates 'PyMol' scripts, and ensures calculations meet publication standards. 'HDXBoxeR' assists in various aspects of hydrogen-deuterium exchange data analysis, including reprocessing data, calculating parameters, identifying significant peptides, generating plots, and facilitating comparison between protein states. For details check papers by Hageman and Weis (2019) <doi:10.1021/acs.analchem.9b01325> and Masson et al. (2019) <doi:10.1038/s41592-019-0459-y>. 'HDXBoxeR' citation: Janowska et al. (2024) <doi:10.1093/bioinformatics/btae479>.

Maintained by Maria K. Janowska. Last updated 7 months ago.

29.5 match 2 stars 4.60 score 3 scripts

r-tmap

tmap:Thematic Maps

Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.

Maintained by Martijn Tennekes. Last updated 5 days ago.

choropleth-maps maps spatial thematic-maps visualisation

7.4 match 880 stars 16.73 score 13k scripts 24 dependents

jonocarroll

ggeasy:Easy Access to 'ggplot2' Commands

Provides a series of aliases to commonly used but difficult to remember 'ggplot2' sequences.

Maintained by Jonathan Carroll. Last updated 4 months ago.

10.1 match 275 stars 10.45 score 652 scripts 6 dependents

tomroh

leaflegend:Add Custom Legends to 'leaflet' Maps

Provides extensions to the 'leaflet' package to customize legends with images, text styling, orientation, sizing, and symbology and functions to create symbols to plot on maps.

Maintained by Thomas Roh. Last updated 8 months ago.

leaflet

10.9 match 35 stars 9.46 score 132 scripts 20 dependents

animint

animint2:Animated Interactive Grammar of Graphics

Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.

Maintained by Toby Hocking. Last updated 27 days ago.

11.2 match 64 stars 8.87 score 173 scripts

jfrench

autoimage:Multiple Heat Maps for Projected Coordinates

Functions for displaying multiple images or scatterplots with a color scale, i.e., heat maps, possibly with projected coordinates. The package relies on the base graphics system, so graphics are rendered rapidly.

Maintained by Joshua French. Last updated 4 years ago.

14.6 match 7 stars 6.73 score 57 scripts 3 dependents

chris-prener

biscale:Tools and Palettes for Bivariate Thematic Mapping

Provides a 'ggplot2' centric approach to bivariate mapping. This is a technique that maps two quantities simultaneously rather than the single value that most thematic maps display. The package provides a suite of tools for calculating breaks using multiple different approaches, a selection of palettes appropriate for bivariate mapping and scale functions for 'ggplot2' calls that adds those palettes to maps. Tools for creating bivariate legends are also included.

Maintained by Christopher Prener. Last updated 3 years ago.

11.4 match 122 stars 8.53 score 466 scripts

symbolixau

mapdeck:Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'

Provides a mechanism to plot an interactive map using 'Mapbox GL' (<https://docs.mapbox.com/mapbox-gl-js/api/>), a javascript library for interactive maps, and 'Deck.gl' (<https://deck.gl/>), a javascript library which uses 'WebGL' for visualising large data sets.

Maintained by David Cooley. Last updated 3 months ago.

deckgl geospatial mapbox mapbox-gl mapbox-gl-js maps cpp

9.0 match 363 stars 10.30 score 368 scripts 1 dependents

hgerritsen

mapplots:Data Visualisation on Maps

Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.

Maintained by Hans Gerritsen. Last updated 2 years ago.

17.9 match 2 stars 4.90 score 442 scripts 3 dependents

ms609

PlotTools:Add Continuous Legends to Plots

Annotate plots with legends for continuous variables and colour spectra using the base graphics plotting tools; and manipulate irregular polygons.

Maintained by Martin R. Smith. Last updated 14 days ago.

legends plotting spectrum

15.5 match 5.30 score 6 scripts 16 dependents

plotly

plotly:Create Interactive Web Graphics via 'plotly.js'

Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.

Maintained by Carson Sievert. Last updated 3 months ago.

d3js data-visualization ggplot2 javascript plotly shiny webgl

4.1 match 2.6k stars 19.43 score 93k scripts 797 dependents

karlines

plot3D:Plotting Multi-Dimensional Data

Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.

Maintained by Karline Soetaert. Last updated 1 years ago.

8.3 match 3 stars 9.59 score 2.1k scripts 78 dependents

johncoene

echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5

Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.

Maintained by David Munoz Tord. Last updated 3 days ago.

echarts hacktoberfest htmlwidget htmlwidgets visualization

6.6 match 603 stars 11.45 score 1.3k scripts 11 dependents

wilkelab

cowplot:Streamlined Plot Theme and Plot Annotations for 'ggplot2'

Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.

Maintained by Claus O. Wilke. Last updated 2 months ago.

3.8 match 714 stars 18.83 score 75k scripts 1.4k dependents

muvisu

biplotEZ:EZ-to-Use Biplots

Provides users with an EZ-to-use platform for representing data with biplots. Currently principal component analysis (PCA), canonical variate analysis (CVA) and simple correspondence analysis (CA) biplots are included. This is accompanied by various formatting options for the samples and axes. Alpha-bags and concentration ellipses are included for visual enhancements and interpretation. For an extensive discussion on the topic, see Gower, J.C., Lubbe, S. and le Roux, N.J. (2011, ISBN: 978-0-470-01255-0) Understanding Biplots. Wiley: Chichester.

Maintained by Sugnet Lubbe. Last updated 6 days ago.

fortran

8.3 match 7 stars 8.39 score 30 scripts 1 dependents

taiyun

corrplot:Visualization of a Correlation Matrix

Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.

Maintained by Taiyun Wei. Last updated 5 months ago.

corrplot visualization

3.9 match 323 stars 17.66 score 28k scripts 517 dependents

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

Maintained by Tim Schäfer. Last updated 4 months ago.

3d brain dti freesurfer mesh mri neuroimaging research surface visualization voxel

10.7 match 66 stars 6.47 score 15 scripts

kof-ch

tstools:A Time Series Toolbox for Official Statistics

Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.

Maintained by Stéphane Bisinger. Last updated 1 years ago.

10.7 match 11 stars 6.47 score 177 scripts

harrelfe

Hmisc:Harrell Miscellaneous

Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.

Maintained by Frank E Harrell Jr. Last updated 7 hours ago.

fortran

3.9 match 210 stars 17.61 score 17k scripts 750 dependents

thomasp85

ggraph:An Implementation of Grammar of Graphics for Graphs and Networks

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

ggplot-extension ggplot2 graph-visualization network-visualization visualization cpp

4.0 match 1.1k stars 16.96 score 9.2k scripts 111 dependents

rstudio

leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library

Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.

Maintained by Joe Cheng. Last updated 13 days ago.

gis leaflet-map spatial

3.7 match 821 stars 17.20 score 39k scripts 178 dependents

ggobi

GGally:Extension to 'ggplot2'

The R package 'ggplot2' is a plotting system based on the grammar of graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.

Maintained by Barret Schloerke. Last updated 10 months ago.

3.8 match 597 stars 16.15 score 17k scripts 154 dependents

walkerke

mapgl:Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'

Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>) and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.

Maintained by Kyle Walker. Last updated 1 days ago.

7.3 match 114 stars 8.06 score 138 scripts

dreamrs

billboarder:Create Interactive Chart with the JavaScript 'Billboard' Library

Provides an 'htmlwidgets' interface to 'billboard.js', a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts. All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.

Maintained by Victor Perrier. Last updated 5 months ago.

data-visualization htmlwidgets

6.1 match 174 stars 9.74 score 96 scripts 4 dependents

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 12 days ago.

openblas cpp

3.8 match 39 stars 14.96 score 2.2k scripts 256 dependents

rstudio

dygraphs:Interface to 'Dygraphs' Interactive Time Series Charting Library

An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.

Maintained by Petr Shevtsov. Last updated 2 years ago.

4.1 match 365 stars 13.48 score 3.6k scripts 65 dependents

brandmaier

ggx:A Natural Language Interface to 'ggplot2'

The 'ggplot2' package is the state-of-the-art toolbox for creating and formatting graphs. However, it is easy to forget how certain formatting commands are named and sometimes users find themselves asking: How do you rotate the x-axis labels again? Or how do you hide the legend...? This package allows users to issue natural language commands related to theme-related styling of plots (colors, font size and such), which then are translated into valid 'ggplot2' commands.

Maintained by Andreas M. Brandmaier. Last updated 2 years ago.

8.2 match 152 stars 6.69 score 16 scripts

rempsyc

rempsyc:Convenience Functions for Psychology

Make your workflow faster and easier. Easily customizable plots (via 'ggplot2'), nice APA tables (following the style of the *American Psychological Association*) exportable to Word (via 'flextable'), easily run statistical tests or check assumptions, and automatize various other tasks.

Maintained by Rémi Thériault. Last updated 1 months ago.

convenience-functions ggplot2 psychology statistics visualization

5.0 match 43 stars 10.68 score 214 scripts 2 dependents

jbengler

tidyplots:Tidy Plots for Scientific Papers

The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.

Maintained by Jan Broder Engler. Last updated 4 days ago.

5.6 match 482 stars 9.40 score 85 scripts

braverock

PerformanceAnalytics:Econometric Tools for Performance and Risk Analysis

Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.

Maintained by Brian G. Peterson. Last updated 3 months ago.

3.3 match 222 stars 15.93 score 4.8k scripts 20 dependents

edzer

hexbin:Hexagonal Binning Routines

Binning and plotting functions for hexagonal bins.

Maintained by Edzer Pebesma. Last updated 4 months ago.

fortran

3.8 match 37 stars 14.00 score 2.4k scripts 114 dependents

teunbrand

ggh4x:Hacks for 'ggplot2'

A 'ggplot2' extension that does a variety of little helpful things. The package extends 'ggplot2' facets through customisation, by setting individual scales per panel, resizing panels and providing nested facets. Also allows multiple colour and fill scales per plot. Also hosts a smaller collection of stats, geoms and axis guides.

Maintained by Teun van den Brand. Last updated 3 months ago.

ggplot-extension ggplot2

3.8 match 616 stars 13.98 score 4.4k scripts 20 dependents

danchaltiel

crosstable:Crosstables for Descriptive Analyses

Create descriptive tables for continuous and categorical variables. Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'. You can also compute effect sizes and statistical tests if needed.

Maintained by Dan Chaltiel. Last updated 2 months ago.

descriptive-statistics flextable frequency-table html-report msword officer

5.0 match 116 stars 10.37 score 340 scripts

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

Maintained by Benoit Thieurmel. Last updated 2 years ago.

3.4 match 549 stars 15.14 score 4.1k scripts 195 dependents

usaid-oha-si

selfdestructin5:Creates SI OHA Mission Director Briefers

Creates a series of data frames that can be passed to a gt() to create the PEPFAR summary tables.

Maintained by Tim Essam. Last updated 26 days ago.

12.0 match 1 stars 3.98 score 21 scripts

andysouth

rworldmap:Mapping Global Data

Enables mapping of country level and gridded user datasets.

Maintained by Andy South. Last updated 2 years ago.

3.8 match 30 stars 11.83 score 3.2k scripts 14 dependents

gforge

forestplot:Advanced Forest Plot Using 'grid' Graphics

Allows the creation of forest plots with advanced features, such as multiple confidence intervals per row, customizable fonts for individual text elements, and flexible confidence interval drawing. It also supports mixing text with mathematical expressions. The package extends the application of forest plots beyond traditional meta-analyses, offering a more general version of the original 'rmeta' package’s forestplot() function. It relies heavily on the 'grid' package for rendering the plots.

Maintained by Max Gordon. Last updated 4 months ago.

forestplot

3.9 match 43 stars 11.47 score 716 scripts 21 dependents

murrayefford

secr:Spatially Explicit Capture-Recapture

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

Maintained by Murray Efford. Last updated 3 days ago.

cpp

4.3 match 3 stars 10.18 score 410 scripts 5 dependents

joshuaulrich

xts:eXtensible Time Series

Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.

Maintained by Joshua M. Ulrich. Last updated 4 months ago.

c time-series

2.3 match 221 stars 18.38 score 12k scripts 654 dependents

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

3.2 match 15 stars 12.60 score 7.7k scripts 295 dependents

sssydysss

TransProR:Analysis and Visualization of Multi-Omics Data

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Maintained by Dongyue Yu. Last updated 20 days ago.

5.4 match 174 stars 7.55 score 34 scripts

bioc

plotgardener:Coordinate-Based Genomic Visualization Package for R

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Maintained by Nicole Kramer. Last updated 5 months ago.

visualization genomeannotation functionalgenomics genomeassembly hic cpp

4.0 match 308 stars 10.16 score 167 scripts 3 dependents

brry

berryFunctions:Function Collection Related to Plotting and Hydrology

Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.

Maintained by Berry Boessenkool. Last updated 1 months ago.

4.3 match 13 stars 9.43 score 350 scripts 16 dependents

qile0317

APackOfTheClones:Visualization of Clonal Expansion for Single Cell Immune Profiles

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.

Maintained by Qile Yang. Last updated 4 months ago.

clonal-analysis immune-repertoire immune-system scrna-seq scrnaseq seurat single-cell single-cell-genomics cpp

6.1 match 15 stars 6.45 score 15 scripts

juba

scatterD3:D3 JavaScript Scatterplot from R

Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive features : panning, zooming, tooltips, etc.

Maintained by Julien Barnier. Last updated 7 months ago.

d3 d3js htmlwidgets shiny

4.3 match 160 stars 8.98 score 125 scripts 4 dependents

hadley

ggvis:Interactive Grammar of Graphics

An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework of 'shiny' and drawing web graphics using 'vega'.

Maintained by Hadley Wickham. Last updated 1 years ago.

5.4 match 1 stars 7.02 score 2.3k scripts 11 dependents

mstrimas

colorist:Coloring Wildlife Distributions in Space-Time

Color and visualize wildlife distributions in space-time using raster data. In addition to enabling display of sequential change in distributions through the use of small multiples, 'colorist' provides functions for extracting several features of interest from a sequence of distributions and for visualizing those features using HCL (hue-chroma-luminance) color palettes. Resulting maps allow for "fair" visual comparison of intensity values (e.g., occurrence, abundance, or density) across space and time and can be used to address questions about where, when, and how consistently a species, group, or individual is likely to be found.

Maintained by Matthew Strimas-Mackey. Last updated 11 months ago.

6.6 match 14 stars 5.60 score 19 scripts

uclahs-cds

BoutrosLab.plotting.general:Functions to Create Publication-Quality Plots

Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.

Maintained by Paul Boutros. Last updated 5 months ago.

4.3 match 12 stars 8.36 score 414 scripts 6 dependents

rspatial

terra:Spatial Data Analysis

Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).

Maintained by Robert J. Hijmans. Last updated 22 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

2.0 match 559 stars 17.64 score 17k scripts 851 dependents

deepayan

lattice:Trellis Graphics for R

A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.

Maintained by Deepayan Sarkar. Last updated 11 months ago.

2.0 match 68 stars 17.33 score 27k scripts 13k dependents

dreamrs

apexcharter:Create Interactive Chart with the JavaScript 'ApexCharts' Library

Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.

Maintained by Victor Perrier. Last updated 25 days ago.

data-visualization htmlwidgets

4.0 match 144 stars 8.51 score 247 scripts

mrjoh3

c3:'C3.js' Chart Library

Create interactive charts with the 'C3.js' <http://c3js.org/> charting library. All plot types in 'C3.js' are available and include line, bar, scatter, and mixed geometry plots. Plot annotations, labels and axis are highly adjustable. Interactive web based charts can be embedded in R Markdown documents or Shiny web applications.

Maintained by Matt Johnson. Last updated 4 years ago.

chart htmlwidget plots

5.3 match 39 stars 6.45 score 72 scripts

palaeoverse

rphylopic:Get Silhouettes of Organisms from PhyloPic

Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>) to fetch silhouette images of organisms. Includes functions for adding silhouettes to both base R plots and ggplot2 plots.

Maintained by William Gearty. Last updated 6 months ago.

base-r ggplot2 phylopic silhouette

3.5 match 91 stars 9.25 score 272 scripts

mages

googleVis:R Interface to Google Charts

R interface to Google's chart tools, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with an Internet connection is required. The data remains local and is not uploaded to Google.

Maintained by Markus Gesmann. Last updated 10 months ago.

2.5 match 361 stars 12.98 score 2.4k scripts 11 dependents

funkyheatmap

funkyheatmap:Generating Funky Heatmaps for Data Frames

Allows generating heatmap-like visualisations for data frames. Funky heatmaps can be fine-tuned by providing annotations of the columns and rows, which allows assigning multiple palettes or geometries or grouping rows and columns together in categories. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.

Maintained by Robrecht Cannoodt. Last updated 1 months ago.

3.9 match 171 stars 8.37 score 76 scripts

bioc

Heatplus:Heatmaps with row and/or column covariates and colored clusters

Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.

Maintained by Alexander Ploner. Last updated 5 months ago.

microarray visualization

4.3 match 7.63 score 94 scripts 5 dependents

kcuilla

reactablefmtr:Streamlined Table Styling and Formatting for Reactable

Provides various features to streamline and enhance the styling of interactive reactable tables with easy-to-use and highly-customizable functions and themes. Apply conditional formatting to cells with data bars, color scales, color tiles, and icon sets. Utilize custom table themes inspired by popular websites such and bootstrap themes. Apply sparkline line & bar charts (note this feature requires the 'dataui' package which can be downloaded from <https://github.com/timelyportfolio/dataui>). Increase the portability and reproducibility of reactable tables by embedding images from the web directly into cells. Save the final table output as a static image or interactive file.

Maintained by Kyle Cuilla. Last updated 2 years ago.

customization data-visualization easy-to-use reproducible tables

3.7 match 209 stars 8.79 score 460 scripts 4 dependents

ncss-tech

soilDB:Soil Database Interface

A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.

Maintained by Andrew Brown. Last updated 7 days ago.

kssl nasis nrcs soil soil-data-access soil-survey soilweb sql usda

2.8 match 87 stars 11.34 score 1.0k scripts 1 dependents

cran

vcd:Visualizing Categorical Data

Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was package was originally inspired by the book "Visualizing Categorical Data" by Michael Friendly and is now the main support package for a new book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer (2015).

Maintained by David Meyer. Last updated 6 months ago.

3.9 match 5 stars 8.19 score 87 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 7 hours ago.

fortran cpp

1.9 match 87 stars 16.70 score 7.7k scripts 99 dependents

kassambara

ggpubr:'ggplot2' Based Publication Ready Plots

The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.

Maintained by Alboukadel Kassambara. Last updated 2 years ago.

1.9 match 1.2k stars 16.68 score 65k scripts 409 dependents

pik-piam

mip:Comparison of multi-model runs

Package contains generic functions to produce comparison plots of multi-model runs.

Maintained by David Klein. Last updated 26 days ago.

3.8 match 1 stars 8.08 score 70 scripts 20 dependents

paulojus

geoR:Analysis of Geostatistical Data

Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.

Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.

4.0 match 10 stars 7.57 score 1.8k scripts 12 dependents

stemangiola

tidyHeatmap:A Tidy Implementation of Heatmap

This is a tidy implementation for heatmap. At the moment it is based on the (great) package 'ComplexHeatmap'. The goal of this package is to interface a tidy data frame with this powerful tool. Some of the advantages are: Row and/or columns colour annotations are easy to integrate just specifying one parameter (column names). Custom grouping of rows is easy to specify providing a grouped tbl. For example: df %>% group_by(...). Labels size adjusted by row and column total number. Default use of Brewer and Viridis palettes.

Maintained by Stefano Mangiola. Last updated 1 months ago.

assaydomain infrastructure brewer complexheatmap custom-palette dplyr graphviz heatmap mtcars plotting rstudio scale tibble tidy tidy-data-frame tidybulk tidyverse viridis

3.0 match 335 stars 10.23 score 197 scripts 1 dependents

lgnbhl

xlcharts:Create Native 'Excel' Charts and Work with Microsoft 'Excel' Files

An R interface to the 'OpenPyXL' 'Python' library to create native 'Excel' charts and work with Microsoft 'Excel' files.

Maintained by Felix Luginbuhl. Last updated 11 days ago.

excel

6.6 match 12 stars 4.48 score 4 scripts

svkucheryavski

mdatools:Multivariate Data Analysis for Chemometrics

Projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics. S. Kucheryavskiy (2020) <doi:10.1016/j.chemolab.2020.103937>.

Maintained by Sergey Kucheryavskiy. Last updated 8 months ago.

3.8 match 35 stars 7.37 score 220 scripts 1 dependents

tkonopka

Rcssplot:Styling of Graphics using Cascading Style Sheets

Provides a means to style plots through cascading style sheets. This separates the aesthetics from the data crunching in plots and charts.

Maintained by Tomasz Konopka. Last updated 4 months ago.

css data-science visualization

5.2 match 10 stars 5.35 score 15 scripts

bioc

PhyloProfile:PhyloProfile

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Maintained by Vinh Tran. Last updated 6 days ago.

software visualization datarepresentation multiplecomparison functionalprediction dimensionreduction bioinformatics heatmap interactive-visualizations orthologs phylogenetic-profile shiny

3.5 match 33 stars 7.77 score 10 scripts

heike

x3ptools:Tools for Working with 3D Surface Measurements

The x3p file format is specified in ISO standard 5436:2000 to describe 3d surface measurements. 'x3ptools' allows reading, writing and basic modifications to the 3D surface measurements.

Maintained by Heike Hofmann. Last updated 6 months ago.

3.7 match 8 stars 7.48 score 281 scripts 2 dependents

ccamlr

CCAMLRGIS:Antarctic Spatial Data Manipulation

Loads and creates spatial data, including layers and tools that are relevant to the activities of the Commission for the Conservation of Antarctic Marine Living Resources. Provides two categories of functions: load functions and create functions. Load functions are used to import existing spatial layers from the online CCAMLR GIS such as the ASD boundaries. Create functions are used to create layers from user data such as polygons and grids.

Maintained by Stephane Thanassekos. Last updated 28 days ago.

4.3 match 7 stars 6.46 score 38 scripts

r-spatial

stars:Spatiotemporal Arrays, Raster and Vector Data Cubes

Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.

Maintained by Edzer Pebesma. Last updated 30 days ago.

raster satellite-images spatial

1.5 match 571 stars 18.27 score 7.2k scripts 137 dependents

bioc

RnBeads:RnBeads

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Maintained by Fabian Mueller. Last updated 1 months ago.

dnamethylation methylationarray methylseq epigenetics qualitycontrol preprocessing batcheffect differentialmethylation sequencing cpgisland immunooncology twochannel dataimport

4.0 match 6.85 score 169 scripts 1 dependents

davidgohel

ggiraph:Make 'ggplot2' Graphics Interactive

Create interactive 'ggplot2' graphics using 'htmlwidgets'.

Maintained by David Gohel. Last updated 3 months ago.

libpng cpp

1.9 match 819 stars 14.39 score 4.1k scripts 34 dependents

martin-borkovec

ggparty:'ggplot' Visualizations for the 'partykit' Package

Extends 'ggplot2' functionality to the 'partykit' package. 'ggparty' provides the necessary tools to create clearly structured and highly customizable visualizations for tree-objects of the class 'party'.

Maintained by Martin Borkovec. Last updated 6 years ago.

2.8 match 146 stars 9.47 score 156 scripts 7 dependents

trafficonese

leaflet.extras:Extra Functionality for 'leaflet' Package

The 'leaflet' JavaScript library provides many plugins some of which are available in the core 'leaflet' package, but there are many more. It is not possible to support them all in the core 'leaflet' package. This package serves as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet' plugins.

Maintained by Sebastian Gatscha. Last updated 2 months ago.

data-visualization geospatial leaflet

2.0 match 218 stars 13.27 score 2.5k scripts 25 dependents

ddediu

AdhereR:Adherence to Medications

Computation of adherence to medications from Electronic Health care Data and visualization of individual medication histories and adherence patterns. The package implements a set of S3 classes and functions consistent with current adherence guidelines and definitions. It allows the computation of different measures of adherence (as defined in the literature, but also several original ones), their publication-quality plotting, the estimation of event duration and time to initiation, the interactive exploration of patient medication history and the real-time estimation of adherence given various parameter settings. It scales from very small datasets stored in flat CSV files to very large databases and from single-thread processing on mid-range consumer laptops to parallel processing on large heterogeneous computing clusters. It exposes a standardized interface allowing it to be used from other programming languages and platforms, such as Python.

Maintained by Dan Dediu. Last updated 1 years ago.

adherence-to-medications electronic-healthcare-data hadoop medical-databases medication-histories python sql visualisation

3.8 match 28 stars 7.07 score 47 scripts 1 dependents

jbkunst

highcharter:A Wrapper for the 'Highcharts' Library

A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.

Maintained by Joshua Kunst. Last updated 1 years ago.

highcharts htmlwidgets shiny shiny-r visualization wrapper

1.9 match 725 stars 13.93 score 4.9k scripts 18 dependents

cran

ggtern:An Extension to 'ggplot2', for the Creation of Ternary Diagrams

Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.

Maintained by Nicholas Hamilton. Last updated 12 months ago.

3.7 match 4 stars 7.05 score 1.1k scripts 6 dependents

riatelab

mapsf:Thematic Cartography

Create and integrate thematic maps in your workflow. This package helps to design various cartographic representations such as proportional symbols, choropleth or typology maps. It also offers several functions to display layout elements that improve the graphic presentation of maps (e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on 'base' graphics.

Maintained by Timothée Giraud. Last updated 4 days ago.

cartography map spatial spatial-analysis

2.3 match 228 stars 11.28 score 414 scripts 11 dependents

yulab-smu

ggbreak:Set Axis Break for 'ggplot2'

An implementation of scale functions for setting axis breaks of a 'gg' plot (S Xu (2021) <doi:10.3389/fgene.2021.774846>).

Maintained by Guangchuang Yu. Last updated 1 months ago.

axis-break cut-plot ggbreak ggplot2 wrap-plot

2.6 match 137 stars 9.81 score 956 scripts 1 dependents

smin95

smplot2:Create Standalone and Composite Plots in 'ggplot2' for Publications

Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.

Maintained by Seung Hyun Min. Last updated 1 months ago.

easy-to-use ggplot2 scientific-visualization visualization

3.5 match 24 stars 7.08 score 288 scripts 1 dependents

hta-pharma

maicplus:Matching Adjusted Indirect Comparison

Facilitates performing matching adjusted indirect comparison (MAIC) analysis where the endpoint of interest is either time-to-event (e.g. overall survival) or binary (e.g. objective tumor response). The method is described by Signorovitch et al (2012) <doi:10.1016/j.jval.2012.05.004>.

Maintained by Isaac Gravestock. Last updated 23 days ago.

3.4 match 5 stars 7.37 score 16 scripts

pepijn-devries

ggsankeyfier:Create Sankey and Alluvial Diagrams Using 'ggplot2'

Sankey and alluvial diagrams visualise flows of quantities across stages in stacked bars. This package makes it easy to create such diagrams using 'ggplot2'.

Maintained by Pepijn de Vries. Last updated 7 months ago.

ggplot2 visualisation

3.5 match 15 stars 7.09 score 59 scripts

trevorld

ggpattern:'ggplot2' Pattern Geoms

Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.

Maintained by Trevor L. Davis. Last updated 2 months ago.

2.0 match 368 stars 12.33 score 1.7k scripts 3 dependents

bioc

destiny:Creates diffusion maps

Create and plot diffusion maps.

Maintained by Philipp Angerer. Last updated 4 months ago.

cellbiology cellbasedassays clustering software visualization diffusion-maps dimensionality-reduction cpp

2.3 match 81 stars 10.94 score 792 scripts

jaimemosg

EstimationTools:Maximum Likelihood Estimation for Probability Functions from Data Sets

Total Time on Test plot and routines for parameter estimation of any lifetime distribution implemented in R via maximum likelihood (ML) given a data set. It is implemented thinking on parametric survival analysis, but it feasible to use in parameter estimation of probability density or mass functions in any field. The main routines 'maxlogL' and 'maxlogLreg' are wrapper functions specifically developed for ML estimation. There are included optimization procedures such as 'nlminb' and 'optim' from base package, and 'DEoptim' Mullen (2011) <doi:10.18637/jss.v040.i06>. Standard errors are estimated with 'numDeriv' Gilbert (2011) <https://CRAN.R-project.org/package=numDeriv> or the option 'Hessian = TRUE' of 'optim' function.

Maintained by Jaime Mosquera. Last updated 1 years ago.

distance-sampling maximum-likelihood-estimation ttt-plot

4.0 match 4 stars 6.07 score 97 scripts 1 dependents

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 2 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

2.0 match 7 stars 12.11 score 241 scripts 227 dependents

usaid-oha-si

glitr:Adorned SI style plots

Helps create and export ggplot2 charts in the style used by the GH OHA SI team. Includes multiple styles and themes to tweak plots to user needs. Sample testing data also available.

Maintained by Tim Essam. Last updated 3 months ago.

3.8 match 27 stars 6.43 score 279 scripts 1 dependents

milesmcbain

inlegend:Inset legend themes for ggplot2 maps

Provides themes for making ggplot2 maps with inset legends and without whitespace around the margins.

Maintained by Miles McBain. Last updated 4 years ago.

7.2 match 41 stars 3.31 score 7 scripts

baptiste

egg:Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size

Miscellaneous functions to help customise 'ggplot2' objects. High-level functions are provided to post-process 'ggplot2' layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom 'geom', and helper functions to enforce symmetric scales or add tags to facetted plots.

Maintained by Baptiste Auguie. Last updated 4 years ago.

2.0 match 13 stars 11.84 score 2.4k scripts 67 dependents

bioc

gmoviz:Seamless visualization of complex genomic variations in GMOs and edited cell lines

Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.

Maintained by Kathleen Zeglinski. Last updated 5 months ago.

visualization sequencing geneticvariability genomicvariation coverage

5.5 match 4.30 score 9 scripts

jacolien

plotfunctions:Various Functions to Facilitate Visualization of Data and Analysis

When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.

Maintained by Jacolien van Rij. Last updated 5 years ago.

5.0 match 4.73 score 94 scripts 7 dependents

cran

SSDforR:Functions to Analyze Single System Data

Functions to visually and statistically analyze single system data.

Maintained by Charles Auerbach. Last updated 3 months ago.

15.8 match 1.48 score

grantmcdermott

tinyplot:Lightweight Extension of the Base R Graphics System

Lightweight extension of the base R graphics system, with support for automatic legends, facets, themes, and various other enhancements.

Maintained by Grant McDermott. Last updated 5 days ago.

2.4 match 310 stars 9.63 score 51 scripts 3 dependents

crazycapivara

deckgl:An R Interface to 'deck.gl'

Makes 'deck.gl' <https://deck.gl/>, a WebGL-powered open-source JavaScript framework for visual exploratory data analysis of large datasets, available within R via the 'htmlwidgets' package. Furthermore, it supports basemaps from 'mapbox' <https://www.mapbox.com/> via 'mapbox-gl-js' <https://github.com/mapbox/mapbox-gl-js>.

Maintained by Stefan Kuethe. Last updated 2 years ago.

deck-gl htmlwidgets mapbox-gl maps rspatial spatial webgl

3.6 match 94 stars 6.40 score 54 scripts

bioc

ggbio:Visualization tools for genomic data

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Maintained by Michael Lawrence. Last updated 5 months ago.

infrastructure visualization

1.9 match 111 stars 12.26 score 734 scripts 17 dependents

lazappi

clustree:Visualise Clusterings at Different Resolutions

Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.

Maintained by Luke Zappia. Last updated 1 years ago.

clustering clustering-trees visualisation visualization

2.0 match 219 stars 11.40 score 1.9k scripts 5 dependents

r4ss

r4ss:R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.

Maintained by Ian G. Taylor. Last updated 5 days ago.

fisheries fisheries-stock-assessment stock-synthesis

2.0 match 43 stars 11.38 score 1.0k scripts 2 dependents

wilkox

treemapify:Draw Treemaps in 'ggplot2'

Provides 'ggplot2' geoms for drawing treemaps.

Maintained by David Wilkins. Last updated 9 months ago.

data-visualisation ggplot2 treemap

1.8 match 215 stars 12.58 score 1.6k scripts 9 dependents

lakshay-anand

chromoMap:Interactive Genomic Visualization of Biological Data

Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the large size of the chromosomes, it is impractical to visualize each element on the same plot. However, the plot provides a magnified view for each of chromosome locus to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.

Maintained by Lakshay Anand. Last updated 3 years ago.

5.0 match 9 stars 4.46 score 80 scripts

maliny12

sugarglider:Create Glyph-Maps of Spatiotemporal Data

Provides 'ggplot2' extensions to construct glyph-maps for visualizing seasonality in spatiotemporal data. See the Journal of Statistical Software reference: Zhang, H. S., Cook, D., Laa, U., Langrené, N., & Menéndez, P. (2024) <doi:10.18637/jss.v110.i07>. The manuscript for this package is currently under preparation and can be found on GitHub at <https://github.com/maliny12/paper-sugarglider>.

Maintained by Maliny Po. Last updated 2 months ago.

data-visualization

3.2 match 11 stars 6.68 score 7 scripts

bioc

cytomapper:Visualization of highly multiplexed imaging data in R

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

Maintained by Lasse Meyer. Last updated 5 months ago.

immunooncology software singlecell onechannel twochannel multiplecomparison normalization dataimport bioimaging imaging-mass-cytometry single-cell spatial-analysis

2.2 match 32 stars 9.61 score 354 scripts 5 dependents

pharmaverse

ggsurvfit:Flexible Time-to-Event Figures

Ease the creation of time-to-event (i.e. survival) endpoint figures. The modular functions create figures ready for publication. Each of the functions that add to or modify the figure are written as proper 'ggplot2' geoms or stat methods, allowing the functions from this package to be combined with any function or customization from 'ggplot2' and other 'ggplot2' extension packages.

Maintained by Daniel D. Sjoberg. Last updated 2 months ago.

2.0 match 76 stars 10.50 score 640 scripts 2 dependents

chrislou-bioinfo

gg.gap:Define Segments in y-Axis for 'ggplot2'

It is not very easy to define segments for y-axis in a 'ggplot2' plot. gg.gap() function in this package can carry it out.

Maintained by Jiacheng Lou. Last updated 5 years ago.

4.1 match 28 stars 5.08 score 86 scripts

cran

caroline:A Collection of Database, Data Structure, Visualization, and Utility Functions for R

The caroline R library contains dozens of functions useful for: database migration (dbWriteTable2), database style joins & aggregation (nerge, groupBy, & bestBy), data structure conversion (nv, tab2df), legend table making (sstable & leghead), automatic legend positioning for scatter and box plots (), plot annotation (labsegs & mvlabs), data visualization (pies, sparge, confound.grid & raPlot), character string manipulation (m & pad), file I/O (write.delim), batch scripting, data exploration, and more. The package's greatest contributions lie in the database style merge, aggregation and interface functions as well as in it's extensive use and propagation of row, column and vector names in most functions.

Maintained by David Schruth. Last updated 5 months ago.

6.3 match 3.29 score 108 scripts 3 dependents

pachadotdev

d3po:Fast and Beautiful Interactive Visualization for 'Markdown' and 'Shiny'

Apache licensed alternative to 'Highcharter' which provides functions for both fast and beautiful interactive visualization for 'Markdown' and 'Shiny'.

Maintained by Mauricio Vargas Sepulveda. Last updated 2 years ago.

htmlwidgets shiny visualization

3.3 match 43 stars 6.31 score 24 scripts

insee-psar-at

oceanis:Cartography for Statistical Analysis

Creating maps for statistical analysis such as proportional circles, choropleth, typology and flows. Some functions use 'shiny' or 'leaflet' technologies for dynamism and interactivity. The great features are : - Create maps in a web environment where the parameters are modifiable on the fly ('shiny' and 'leaflet' technologies). - Create interactive maps through zoom and pop-up ('leaflet' technology). - Create frozen maps with the possibility to add labels.

Maintained by Sébastien Novella. Last updated 1 months ago.

3.6 match 12 stars 5.79 score 17 scripts

rhenkin

vfinputs:Visual Filter Inputs for Shiny

A set of visual input controls for Shiny apps to facilitate filtering across multiple outputs.

Maintained by Rafael Henkin. Last updated 4 years ago.

interactive shiny visualization

7.7 match 1 stars 2.70 score 7 scripts

lbb220

GISTools:Further Capabilities in Geographic Information Science

Mapping and spatial data manipulation tools - in particular drawing thematic maps with nice looking legends, and aggregation of point data to polygons.

Maintained by Binbin Lu. Last updated 6 months ago.

5.0 match 4.07 score 584 scripts

jvg0mes

metools:Macroeconomics Tools

Provides a number of functions to facilitate the handling and production of reports using time series data. The package was developed to be understandable for beginners, so some functions aim to transform processes that would be complex into functions with a few lines. The main advantage of using the 'metools' package is the ease of producing reports and working with time series using a few lines of code, so the code is clean and easy to understand/maintain. Learn more about the 'metools' at <https://metoolsr.wordpress.com>.

Maintained by João Victor Gomes de Araujo Santana. Last updated 5 years ago.

7.5 match 2.70 score

karlines

shape:Functions for Plotting Graphical Shapes, Colors

Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

Maintained by Karline Soetaert. Last updated 1 years ago.

1.9 match 10.86 score 984 scripts 1.4k dependents

bioc

ggcyto:Visualize Cytometry data with ggplot

With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology flowcytometry cellbasedassays infrastructure visualization

1.8 match 58 stars 11.25 score 362 scripts 5 dependents

cran

IDPmisc:'Utilities of Institute of Data Analyses and Process Design (www.zhaw.ch/idp)'

Different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with differently colored margin and plot region. In addition, the package contains auxiliary functions for data manipulation like omitting observations with irregular values or selecting data by logical vectors, which include NAs. Other functions are especially useful in spectroscopy and analyses of environmental data: robust baseline fitting, finding peaks in spectra, converting humidity measures.

Maintained by Christoph Hofer. Last updated 1 years ago.

5.4 match 1 stars 3.64 score 22 dependents

rolkra

explore:Simplifies Exploratory Data Analysis

Interactive data exploration with one line of code, automated reporting or use an easy to remember set of tidy functions for low code exploratory data analysis.

Maintained by Roland Krasser. Last updated 3 months ago.

data-exploration data-visualisation decision-trees eda rmarkdown shiny tidy

1.7 match 228 stars 11.43 score 221 scripts 1 dependents

bioc

pRoloc:A unifying bioinformatics framework for spatial proteomics

The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.

Maintained by Lisa Breckels. Last updated 27 days ago.

immunooncology proteomics massspectrometry classification clustering qualitycontrol bioconductor proteomics-data spatial-proteomics visualisation openblas cpp

2.3 match 15 stars 8.71 score 101 scripts 2 dependents

davidhodge931

ggblanket:Simplify 'ggplot2' Visualisation

Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.

Maintained by David Hodge. Last updated 6 days ago.

data-visualisation data-visualization ggplot ggplot-extension ggplot2 ggplot2-enhancements visualisation visualization

2.3 match 170 stars 8.43 score 45 scripts

cran

VCA:Variance Component Analysis

ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features.

Maintained by Andre Schuetzenmeister. Last updated 1 years ago.

fortran openblas

4.3 match 2 stars 4.51 score 5 dependents

wraff

wrGraph:Graphics in the Context of Analyzing High-Throughput Data

Additional options for making graphics in the context of analyzing high-throughput data are available here. This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots, automatic checking for optimal location of legends in plots, small histograms to insert as legends, histograms re-transforming axis labels to linear when plotting log2-transformed data, a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats, principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples, generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>, staggered count plots and generation of mouse-over interactive html pages.

Maintained by Wolfgang Raffelsberger. Last updated 4 months ago.

9.5 match 2.00 score 6 scripts

ropensci

drake:A Pipeline Toolkit for Reproducible Computation at Scale

A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://docs.ropensci.org/drake/> and the online manual <https://books.ropensci.org/drake/>.

Maintained by William Michael Landau. Last updated 3 months ago.

data-science drake high-performance-computing makefile peer-reviewed pipeline reproducibility reproducible-research ropensci workflow

1.7 match 1.3k stars 11.49 score 1.7k scripts 1 dependents

tconwell

html5:Creates Valid HTML5 Strings

Generates valid HTML tag strings for HTML5 elements documented by Mozilla. Attributes are passed as named lists, with names being the attribute name and values being the attribute value. Attribute values are automatically double-quoted. To declare a DOCTYPE, wrap html() with function doctype(). Mozilla's documentation for HTML5 is available here: <https://developer.mozilla.org/en-US/docs/Web/HTML/Element>. Elements marked as obsolete are not included.

Maintained by Timothy Conwell. Last updated 2 years ago.

5.2 match 1 stars 3.65 score 1 scripts 3 dependents

antoineguillot2

D3partitionR:Interactive Charts of Nested and Hierarchical Data with 'D3.js'

Builds interactive 'd3.js' hierarchical visualisation easily. D3partitionR makes it easy to build and customize sunburst, circle treemap, treemap, partition chart, ...

Maintained by Antoine Guillot. Last updated 6 years ago.

d3js d3partitionr data-visualization r-shiny

4.3 match 40 stars 4.30 score 8 scripts

federico-m-stefanini

convergEU:Monitoring Convergence of EU Countries

Indicators and measures by country and time describe what happens at economic and social levels. This package provides functions to calculate several measures of convergence after imputing missing values. The automated downloading of Eurostat data, followed by the production of country fiches and indicator fiches, makes possible to produce automated reports. The Eurofound report (<doi:10.2806/68012>) "Upward convergence in the EU: Concepts, measurements and indicators", 2018, is a detailed presentation of convergence.

Maintained by Federico M. Stefanini. Last updated 2 years ago.

3.8 match 1 stars 4.95 score 89 scripts

hms-dbmi

UpSetR:A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets

Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.

Maintained by Jake Conway. Last updated 4 years ago.

gehlenborglab ggplot2 upset upsetr visualization

1.2 match 781 stars 15.33 score 4.8k scripts 42 dependents

kleebaum

geoelectrics:3D-Visualization of Geoelectric Resistivity Measurement Profiles

Visualizes two-dimensional geoelectric resistivity measurement profiles in three dimensions.

Maintained by Anja Kleebaum. Last updated 2 years ago.

4.3 match 13 stars 4.28 score 29 scripts

bioc

gtrellis:Genome Level Trellis Layout

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing

2.2 match 39 stars 8.24 score 37 scripts 1 dependents

reconhub

incidence:Compute, Handle, Plot and Model Incidence of Dated Events

Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

Maintained by Tim Taylor. Last updated 7 months ago.

outbreak

1.5 match 58 stars 12.06 score 504 scripts 11 dependents

bioc

marray:Exploratory analysis for two-color spotted microarray data

Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.

Maintained by Yee Hwa (Jean) Yang. Last updated 5 months ago.

microarray twochannel preprocessing

2.0 match 8.92 score 222 scripts 37 dependents

r-forge

CHNOSZ:Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also implements a group additivity algorithm for the standard thermodynamic properties of proteins.

Maintained by Jeffrey Dick. Last updated 8 days ago.

fortran

1.9 match 9.46 score 238 scripts 4 dependents

alexym1

fusionchartsR:Embedding FusionCharts in R

FusionCharts provides awesome and minimalist functions to make beautiful interactive charts <https://www.fusioncharts.com/>.

Maintained by Alex Yahiaoui Martinez. Last updated 3 months ago.

4.0 match 6 stars 4.40 score 42 scripts

rmaia

pavo:Perceptual Analysis, Visualization and Organization of Spectral Colour Data

A cohesive framework for the spectral and spatial analysis of colour described in Maia, Eliason, Bitton, Doucet & Shawkey (2013) <doi:10.1111/2041-210X.12069> and Maia, Gruson, Endler & White (2019) <doi:10.1111/2041-210X.13174>.

Maintained by Thomas White. Last updated 1 months ago.

1.8 match 72 stars 9.72 score 151 scripts 1 dependents

samuel-marsh

scCustomize:Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.

Maintained by Samuel Marsh. Last updated 3 months ago.

customization ggplot2 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization

2.0 match 242 stars 8.75 score 1.1k scripts

sahirbhatnagar

casebase:Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression

Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival curves for a given covariate profile. This approach accommodates any log-linear hazard function of prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide a plot method for visualizing incidence density via population time plots. Based on the case-base sampling approach of Hanley and Miettinen (2009) <DOI:10.2202/1557-4679.1125>, Saarela and Arjas (2015) <DOI:10.1111/sjos.12125>, and Saarela (2015) <DOI:10.1007/s10985-015-9352-x>.

Maintained by Sahir Bhatnagar. Last updated 7 months ago.

competing-risks cox-regression regression-models survival-analysis

2.4 match 9 stars 7.16 score 94 scripts

hrbrmstr

vegalite:Tools to Encode Visualizations with the 'Grammar of Graphics'-Like 'Vega-Lite' 'Spec'

The 'Vega-Lite' 'JavaScript' framework provides a higher-level grammar for visual analysis, akin to 'ggplot' or 'Tableau', that generates complete 'Vega' specifications. Functions exist which enable building a valid 'spec' from scratch or importing a previously created 'spec' file. Functions also exist to export 'spec' files and to generate code which will enable plots to be embedded in properly configured web pages. The default behavior is to generate an 'htmlwidget'.

Maintained by Bob Rudis. Last updated 7 years ago.

data-visualization datavisualization vega-lite vega-lite-spec visualization widget

2.3 match 158 stars 7.60 score 84 scripts

thej022214

corHMM:Hidden Markov Models of Character Evolution

Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.

Maintained by Jeremy Beaulieu. Last updated 27 days ago.

1.8 match 12 stars 9.48 score 422 scripts 2 dependents

jessicaweiss

swimplot:Tools for Creating Swimmers Plots using 'ggplot2'

Used for creating swimmers plots with functions to customize the bars, add points, add lines, add text, and add arrows.

Maintained by Jessica Weiss. Last updated 4 years ago.

4.5 match 2 stars 3.76 score 29 scripts

tongzhou2017

itol.toolkit:Helper Functions for 'Interactive Tree Of Life'

The 'Interactive Tree Of Life' <https://itol.embl.de/> online server can edit and annotate trees interactively. The 'itol.toolkit' package can support all types of annotation templates.

Maintained by Tong Zhou. Last updated 3 months ago.

bioinformatics itol visualization

2.3 match 167 stars 7.48 score 60 scripts

matthewkling

colors3d:Generate 2D and 3D Color Palettes

Generate multivariate color palettes to represent two-dimensional or three-dimensional data in graphics (in contrast to standard color palettes that represent just one variable). You tell 'colors3d' how to map color space onto your data, and it gives you a color for each data point. You can then use these colors to make plots in base 'R', 'ggplot2', or other graphics frameworks.

Maintained by Matthew Kling. Last updated 1 years ago.

5.2 match 3 stars 3.18 score 2 scripts

dardisco

survMisc:Miscellaneous Functions for Survival Data

A collection of functions to help in the analysis of right-censored survival data. These extend the methods available in package:survival.

Maintained by Chris Dardis. Last updated 5 years ago.

1.8 match 1 stars 9.49 score 218 scripts 55 dependents

acorg

Racmacs:Antigenic Cartography Macros

A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.

Maintained by Sam Wilks. Last updated 9 months ago.

openblas cpp openmp

2.0 match 21 stars 8.06 score 362 scripts

epiforecasts

socialmixr:Social Mixing Matrices for Infectious Disease Modelling

Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.

Maintained by Sebastian Funk. Last updated 5 months ago.

1.7 match 38 stars 9.74 score 227 scripts 1 dependents

mindthegap-erc

admtools:Estimate and Manipulate Age-Depth Models

Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain.

Maintained by Niklas Hohmann. Last updated 3 months ago.

age-depth-model geochronology sedimentology stratigraphy

2.3 match 4 stars 7.01 score 34 scripts 1 dependents

adeverse

adegraphics:An S4 Lattice-Based Package for the Representation of Multivariate Data

Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.

Maintained by Aurélie Siberchicot. Last updated 8 months ago.

1.5 match 9 stars 10.37 score 386 scripts 6 dependents

ips-lmu

emuR:Main Package of the EMU Speech Database Management System

Provide the EMU Speech Database Management System (EMU-SDMS) with database management, data extraction, data preparation and data visualization facilities. See <https://ips-lmu.github.io/The-EMU-SDMS-Manual/> for more details.

Maintained by Markus Jochim. Last updated 1 years ago.

2.3 match 24 stars 6.89 score 135 scripts 1 dependents

jokergoo

spiralize:Visualize Data on Spirals

It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>, makes so-called spiral graph or spiral chart. It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high resolution. 2. It is efficient for time series data to reveal periodic patterns.

Maintained by Zuguang Gu. Last updated 9 months ago.

2.0 match 148 stars 7.67 score 35 scripts 3 dependents

stla

rAmCharts4:Interface to the JavaScript Library 'amCharts 4'

Creates JavaScript charts. The charts can be included in 'Shiny' apps and R markdown documents, or viewed from the R console and 'RStudio' viewer. Based on the JavaScript library 'amCharts 4' and the R packages 'htmlwidgets' and 'reactR'. Currently available types of chart are: vertical and horizontal bar chart, radial bar chart, stacked bar chart, vertical and horizontal Dumbbell chart, line chart, scatter chart, range area chart, gauge chart, boxplot chart, pie chart, and 100% stacked bar chart.

Maintained by Stéphane Laurent. Last updated 2 years ago.

amcharts htmlwidgets shiny

3.3 match 28 stars 4.61 score 29 scripts

timelyportfolio

sunburstR:Sunburst 'Htmlwidget'

Make interactive 'd3.js' sequence sunburst diagrams in R with the convenience and infrastructure of an 'htmlwidget'.

Maintained by Kent Russell. Last updated 2 years ago.

chart d3 htmlwidgets interactive javascript visualization

1.5 match 210 stars 10.02 score 310 scripts 4 dependents

johnxhobbs

paletteknife:Create Colour Scales and Legend from Continuous or Categorical Vectors

Streamlines the steps for adding colour scales and associated legends when working with base R graphics, especially for interactive use. Popular palettes are included and pretty legends produced when mapping a large variety of vector classes to a colour scale. An additional helper for adding axes and grid lines complements the base::plot() work flow.

Maintained by John Hobbs. Last updated 3 years ago.

5.5 match 2.70 score 1 scripts

n8thangreen

BCEA:Bayesian Cost Effectiveness Analysis

Produces an economic evaluation of a sample of suitable variables of cost and effectiveness / utility for two or more interventions, e.g. from a Bayesian model in the form of MCMC simulations. This package computes the most cost-effective alternative and produces graphical summaries and probabilistic sensitivity analysis, see Baio et al (2017) <doi:10.1007/978-3-319-55718-2>.

Maintained by Gianluca Baio. Last updated 2 months ago.

bayesian cost-effectiveness

1.5 match 3 stars 9.90 score 243 scripts 3 dependents

traminer

TraMineR:Trajectory Miner: a Sequence Analysis Toolkit

Set of sequence analysis tools for manipulating, describing and rendering categorical sequences, and more generally mining sequence data in the field of social sciences. Although this sequence analysis package is primarily intended for state or event sequences that describe time use or life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and functions for extracting the most frequent event subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.

Maintained by Gilbert Ritschard. Last updated 3 months ago.

cpp

1.8 match 11 stars 8.24 score 534 scripts 13 dependents

symbolixau

googleway:Accesses Google Maps APIs to Retrieve Data and Plot Maps

Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.

Maintained by David Cooley. Last updated 6 months ago.

google-map google-maps google-maps-api google-maps-javascript-api spatial spatial-analysis

1.5 match 236 stars 9.67 score 536 scripts 2 dependents

datastorm-open

rAmCharts:JavaScript Charts Tool

Provides an R interface for using 'AmCharts' Library. Based on 'htmlwidgets', it provides a global architecture to generate 'JavaScript' source code for charts. Most of classes in the library have their equivalent in R with S4 classes; for those classes, not all properties have been referenced but can easily be added in the constructors. Complex properties (e.g. 'JavaScript' object) can be passed as named list. See examples at <https://datastorm-open.github.io/introduction_ramcharts/> and <https://www.amcharts.com/> for more information about the library. The package includes the free version of 'AmCharts' Library. Its only limitation is a small link to the web site displayed on your charts. If you enjoy this library, do not hesitate to refer to this page <https://www.amcharts.com/online-store/> to purchase a licence, and thus support its creators and get a period of Priority Support. See also <https://www.amcharts.com/about/> for more information about 'AmCharts' company.

Maintained by Benoit Thieurmel. Last updated 2 months ago.

2.0 match 49 stars 7.17 score 153 scripts 4 dependents

nvelden

geneviewer:Gene Cluster Visualizations

Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.

Maintained by Niels van der Velden. Last updated 30 days ago.

genetics

2.4 match 69 stars 5.99 score 13 scripts

cran

arcpullr:Pull Data from an 'ArcGIS REST' API

Functions to efficiently query 'ArcGIS REST' APIs <https://developers.arcgis.com/rest/>. Both spatial and SQL queries can be used to retrieve data. Simple Feature (sf) objects are utilized to perform spatial queries. This package was neither produced nor is maintained by Esri.

Maintained by Paul Frater. Last updated 1 months ago.

3.6 match 3.95 score 1 dependents

yunuuuu

ggalign:A 'ggplot2' Extension for Consistent Axis Alignment

A 'ggplot2' extension offers various tools the creation of complex, multi-plot visualizations. Built on the familiar grammar of graphics, it provides intuitive tools to align and organize plots, making it ideal for complex visualizations. It excels in multi-omics research—such as genomics and microbiomes—by simplifying the visualization of intricate relationships between datasets, for example, linking genes to pathways. Whether you need to stack plots, arrange them around a central figure, or create a circular layout, 'ggalign' delivers flexibility and accuracy with minimal effort.

Maintained by Yun Peng. Last updated 18 hours ago.

complex-heatmaps dendrogram dendrogram-heatmap ggplot ggplot-extension ggplot2 heatmap heatmap-visualization heatmaps marginal-plots oncoplot oncoprint tanglegram upset upsetplot

2.0 match 267 stars 7.08 score 27 scripts

bioc

EnhancedVolcano:Publication-ready volcano plots with enhanced colouring and labeling

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.

Maintained by Kevin Blighe. Last updated 5 months ago.

rnaseq geneexpression transcription differentialexpression immunooncology

1.2 match 422 stars 11.68 score 2.7k scripts

blue-matter

MSEtool:Management Strategy Evaluation Toolkit

Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).

Maintained by Adrian Hordyk. Last updated 26 days ago.

cpp

1.8 match 8 stars 7.69 score 163 scripts 3 dependents

mnbram

gggibbous:Moon Charts, a Pie Chart Alternative

Moon charts are like pie charts except that the proportions are shown as crescent or gibbous portions of a circle, like the lit and unlit portions of the moon. As such, they work best with only one or two groups. 'gggibbous' extends 'ggplot2' to allow for plotting multiple moon charts in a single panel and does not require a square coordinate system.

Maintained by Michael Bramson. Last updated 4 years ago.

1.9 match 65 stars 7.38 score 61 scripts 4 dependents

dreamrs

vchartr:Interactive Charts with the 'JavaScript' 'VChart' Library

Provides an 'htmlwidgets' interface to 'VChart.js'. 'VChart', more than just a cross-platform charting library, but also an expressive data storyteller. 'VChart' examples and documentation are available here: <https://www.visactor.io/vchart>.

Maintained by Victor Perrier. Last updated 2 months ago.

2.0 match 9 stars 6.89 score 96 scripts

cran

oaPlots:OpenAnalytics Plots Package

Offers a suite of functions for enhancing R plots.

Maintained by Jason Waddell. Last updated 9 years ago.

13.7 match 1.00 score

marlonecobos

nichevol:Tools for Ecological Niche Evolution Assessment Considering Uncertainty

A collection of tools that allow users to perform critical steps in the process of assessing ecological niche evolution over phylogenies, with uncertainty incorporated explicitly in reconstructions. The method proposed here for ancestral reconstruction of ecological niches characterizes species' niches using a bin-based approach that incorporates uncertainty in estimations. Compared to other existing methods, the approaches presented here reduce risk of overestimation of amounts and rates of ecological niche evolution. The main analyses include: initial exploration of environmental data in occurrence records and accessible areas, preparation of data for phylogenetic analyses, executing comparative phylogenetic analyses of ecological niches, and plotting for interpretations. Details on the theoretical background and methods used can be found in: Owens et al. (2020) <doi:10.1002/ece3.6359>, Peterson et al. (1999) <doi:10.1126/science.285.5431.1265>, Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4>, Peterson (2011) <doi:10.1111/j.1365-2699.2010.02456.x>, Barve et al. (2011) <doi:10.1111/ecog.02671>, Machado-Stredel et al. (2021) <doi:10.21425/F5FBG48814>, Owens et al. (2013) <doi:10.1016/j.ecolmodel.2013.04.011>, Saupe et al. (2018) <doi:10.1093/sysbio/syx084>, and Cobos et al. (2021) <doi:10.1111/jav.02868>.

Maintained by Marlon E. Cobos. Last updated 2 years ago.

3.5 match 14 stars 3.85 score 2 scripts

teunbrand

ggarrow:Arrows for 'ggplot2'

A 'ggplot2' extension that adds specialised arrow geometry layers. It offers more arrow options than the standard 'grid' arrows that are built-in many line-based geom layers.

Maintained by Teun van den Brand. Last updated 9 months ago.

ggplot-extension ggplot2 ggplot2-geom

1.9 match 54 stars 7.17 score 61 scripts 1 dependents

openanalytics

patientProfilesVis:Visualization of Patient Profiles

Creation of patient profile visualizations for exploration, diagnostic or monitoring purposes during a clinical trial. These static visualizations display a patient-specific overview of the evolution during the trial time frame of parameters of interest (as laboratory, ECG, vital signs), presence of adverse events, exposure to a treatment; associated with metadata patient information, as demography, concomitant medication. The visualizations can be tailored for specific domain(s) or endpoint(s) of interest. Visualizations are exported into patient profile report(s) or can be embedded in custom report(s).

Maintained by Laure Cougnaud. Last updated 9 months ago.

2.6 match 7 stars 5.15 score 9 scripts

rudeboybert

SpatialEpi:Methods and Data for Spatial Epidemiology

Methods and data for cluster detection and disease mapping.

Maintained by Albert Y. Kim. Last updated 2 years ago.

cpp

2.0 match 31 stars 6.68 score 146 scripts

syncrosim

rsyncrosim:The R Interface to 'SyncroSim'

'SyncroSim' is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to 'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).

Maintained by Katie Birchard. Last updated 9 days ago.

1.9 match 9 stars 7.09 score 189 scripts

egenn

rtemis:Machine Learning and Visualization

Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.

Maintained by E.D. Gennatas. Last updated 1 months ago.

data-science data-visualization machine-learning machine-learning-library visualization

1.9 match 145 stars 7.09 score 50 scripts 2 dependents

maressyl

LPS:Linear Predictor Score, for Binary Inference from Multiple Continuous Variables

An implementation of the Linear Predictor Score approach, as initiated by Radmacher et al. (J Comput Biol 2001) and enhanced by Wright et al. (PNAS 2003) for gene expression signatures. Several tools for unsupervised clustering of gene expression data are also provided.

Maintained by Sylvain Mareschal. Last updated 4 years ago.

3.5 match 1 stars 3.74 score 11 scripts

bioc

SpatialOmicsOverlay:Spatial Overlay for Omic Data from Nanostring GeoMx Data

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

Maintained by Maddy Griswold. Last updated 5 months ago.

geneexpression transcription cellbasedassays dataimport transcriptomics proteomics proprietaryplatforms rnaseq spatial datarepresentation visualization openjdk

3.1 match 4.30 score 8 scripts

jamesliley

SPARRAfairness:Analysis of Differential Behaviour of SPARRA Score Across Demographic Groups

The SPARRA risk score (Scottish Patients At Risk of admission and Re-Admission) estimates yearly risk of emergency hospital admission using electronic health records on a monthly basis for most of the Scottish population. This package implements a suite of functions used to analyse the behaviour and performance of the score, focusing particularly on differential performance over demographically-defined groups. It includes useful utility functions to plot receiver-operator-characteristic, precision-recall and calibration curves, draw stock human figures, estimate counterfactual quantities without the need to re-compute risk scores, to simulate a semi-realistic dataset.

Maintained by James Liley. Last updated 4 months ago.

4.9 match 2.70 score 4 scripts

asa12138

pcutils:Some Useful Functions for Statistics and Visualization

Offers a range of utilities and functions for everyday programming tasks. 1.Data Manipulation. Such as grouping and merging, column splitting, and character expansion. 2.File Handling. Read and convert files in popular formats. 3.Plotting Assistance. Helpful utilities for generating color palettes, validating color formats, and adding transparency. 4.Statistical Analysis. Includes functions for pairwise comparisons and multiple testing corrections, enabling perform statistical analyses with ease. 5.Graph Plotting, Provides efficient tools for creating doughnut plot and multi-layered doughnut plot; Venn diagrams, including traditional Venn diagrams, upset plots, and flower plots; Simplified functions for creating stacked bar plots, or a box plot with alphabets group for multiple comparison group.

Maintained by Chen Peng. Last updated 5 months ago.

2.0 match 22 stars 6.57 score 28 scripts 4 dependents

bioc

bioCancer:Interactive Multi-Omics Cancers Data Visualization and Analysis

This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.

Maintained by Karim Mezhoud. Last updated 5 months ago.

gui datarepresentation network multiplecomparison pathways reactome visualization geneexpression genetarget analysis biocancer-interface cancer cancer-studies rmarkdown

2.2 match 20 stars 5.95 score 7 scripts

jonathanlees

GEOmap:Topographic and Geologic Mapping

Set of routines for making map projections (forward and inverse), topographic maps, perspective plots, geological maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.

Maintained by Jonathan M. Lees. Last updated 8 months ago.

3.9 match 3.38 score 162 scripts 3 dependents

bioc

trackViewer:A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

Maintained by Jianhong Ou. Last updated 2 months ago.

visualization

1.5 match 8.71 score 145 scripts 2 dependents

bioc

tricycle:tricycle: Transferable Representation and Inference of cell cycle

The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.

Maintained by Shijie Zheng. Last updated 5 months ago.

singlecell software transcriptomics rnaseq transcription biologicalquestion dimensionreduction immunooncology

2.0 match 24 stars 6.52 score 46 scripts

usccana

netplot:Beautiful Graph Drawing

A graph visualization engine that emphasizes on aesthetics at the same time providing default parameters that yield out-of-the-box-nice visualizations. The package is built on top of 'The Grid Graphics Package' and seamlessly work with 'igraph' and 'network' objects.

Maintained by George Vega Yon. Last updated 4 months ago.

graph-visualization igraph netsci network-analysis network-visualization sna statnet

1.9 match 51 stars 6.90 score 78 scripts

rishvish

PieGlyph:Axis Invariant Scatter Pie Plots

Extends 'ggplot2' to help replace points in a scatter plot with pie-chart glyphs showing the relative proportions of different categories. The pie glyphs are independent of the axes and plot dimensions, to prevent distortions when the plot dimensions are changed.

Maintained by Rishabh Vishwakarma. Last updated 9 months ago.

1.9 match 5 stars 6.88 score 29 scripts 1 dependents

adrientaudiere

MiscMetabar:Miscellaneous Functions for Metabarcoding Analysis

Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.

Maintained by Adrien Taudière. Last updated 25 days ago.

sequencing microbiome metagenomics clustering classification visualization amplicon amplicon-sequencing biodiversity-informatics ecology illumina metabarcoding ngs-analysis

2.0 match 17 stars 6.44 score 23 scripts

ropensci

lingtypology:Linguistic Typology and Mapping

Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.

Maintained by George Moroz. Last updated 5 months ago.

abvd afbo atlas autotype bivaltyp clld glottolog-database linguistic-maps linguistics phoible sails typology wals

1.3 match 51 stars 9.58 score 694 scripts

vinhdizzo

IRexamples:Collection of Practical Institutional Research Examples and Tutorials

Provides examples of code for analyzing data or accomplishing tasks that may be useful to institutional or educational researchers.

Maintained by Vinh Nguyen. Last updated 2 years ago.

2.5 match 4 stars 5.00 score 4 scripts

bioc

pathlinkR:Analyze and interpret RNA-Seq results

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

Maintained by Travis Blimkie. Last updated 3 months ago.

genesetenrichment network pathways reactome rnaseq networkenrichment bioinformatics networks pathway-enrichment-analysis visualization

1.9 match 26 stars 6.62 score 2 scripts

swarchal

platetools:Tools and Plots for Multi-Well Plates

Collection of functions for working with multi-well microtitre plates, mainly 96, 384 and 1536 well plates.

Maintained by Scott Warchal. Last updated 1 years ago.

biology ggplot2 lab

2.0 match 54 stars 6.20 score 146 scripts

toxpi

toxpiR:Create ToxPi Prioritization Models

Enables users to build 'ToxPi' prioritization models and provides functionality within the grid framework for plotting ToxPi graphs. 'toxpiR' allows for more customization than the 'ToxPi GUI' (<https://toxpi.org>) and integration into existing workflows for greater ease-of-use, reproducibility, and transparency. toxpiR package behaves nearly identically to the GUI; the package documentation includes notes about all differences. The vignettes download example files from <https://github.com/ToxPi/ToxPi-example-files>.

Maintained by Jonathon F Fleming. Last updated 7 months ago.

data-science modeling toxicology

1.9 match 11 stars 6.58 score 19 scripts

mazamascience

AirMonitor:Air Quality Data Analysis

Utilities for working with hourly air quality monitoring data with a focus on small particulates (PM2.5). A compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Algorithms to calculate NowCast and the associated Air Quality Index (AQI) are defined at the US Environmental Projection Agency AirNow program: <https://document.airnow.gov/technical-assistance-document-for-the-reporting-of-daily-air-quailty.pdf>.

Maintained by Jonathan Callahan. Last updated 6 months ago.

1.9 match 7 stars 6.57 score 178 scripts

bioc

PCAtools:PCAtools: Everything Principal Components Analysis

Principal Component Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This 'summary' of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular - users can also identify optimal number of principal components via different metrics, such as elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.

Maintained by Kevin Blighe. Last updated 5 months ago.

rnaseq atacseq geneexpression transcription singlecell principalcomponent cpp

1.1 match 343 stars 11.12 score 832 scripts 2 dependents

rnabioco

ggtrace:Trace and Highlight Groups of Data Points

Provides 'ggplot2' geoms that allow groups of data points to be outlined or highlighted for emphasis. This is particularly useful when working with dense datasets that are prone to overplotting.

Maintained by Ryan Sheridan. Last updated 1 years ago.

ggplot2 ggplot2-geom visualization

2.0 match 15 stars 6.06 score 38 scripts

cran

espadon:Easy Study of Patient DICOM Data in Oncology

Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.

Maintained by Cathy Fontbonne. Last updated 1 months ago.

cpp

4.3 match 2.85 score

bioc

RedeR:Interactive visualization and manipulation of nested networks

RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.

Maintained by Mauro Castro. Last updated 5 months ago.

gui graphandnetwork network networkenrichment networkinference software systemsbiology

1.8 match 6.65 score 107 scripts 7 dependents

rte-antares-rpackage

antaresViz:Antares Visualizations

Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help 'Antares' users visually explore the results of their simulations.

Maintained by Tatiana Vargas. Last updated 2 months ago.

adequacy bilan dygraphs electric energy leaflet linear-programming manipulatewidge monte-carlo-simulation optimization plotly previsionnel renewable-energy rte shiny shiny-apps simulation stochastic-simulation-algorithm tyndp

1.8 match 21 stars 6.83 score 32 scripts

dfriend21

quadtree:Region Quadtrees for Spatial Data

Provides functionality for working with raster-like quadtrees (also called “region quadtrees”), which allow for variable-sized cells. The package allows for flexibility in the quadtree creation process. Several functions defining how to split and aggregate cells are provided, and custom functions can be written for both of these processes. In addition, quadtrees can be created using other quadtrees as “templates”, so that the new quadtree's structure is identical to the template quadtree. The package also includes functionality for modifying quadtrees, querying values, saving quadtrees to a file, and calculating least-cost paths using the quadtree as a resistance surface.

Maintained by Derek Friend. Last updated 2 years ago.

cpp

1.9 match 19 stars 6.34 score 58 scripts

predictiveecology

quickPlot:A System of Plotting Optimized for Speed and Modularity

A high-level plotting system, compatible with `ggplot2` objects, maps from `sf`, `terra`, `raster`, `sp`. It is built primarily on the 'grid' package. The objective of the package is to provide a plotting system that is built for speed and modularity. This is useful for quick visualizations when testing code and for plotting multiple figures to the same device from independent sources that may be independent of one another (i.e., different function or modules the create the visualizations). The suggested package 'fastshp' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 4 months ago.

plotting visualization

1.5 match 6 stars 7.92 score 121 scripts 12 dependents

sachsmc

causaloptim:An Interface to Specify Causal Graphs and Compute Bounds on Causal Effects

When causal quantities are not identifiable from the observed data, it still may be possible to bound these quantities using the observed data. We outline a class of problems for which the derivation of tight bounds is always a linear programming problem and can therefore, at least theoretically, be solved using a symbolic linear optimizer. We extend and generalize the approach of Balke and Pearl (1994) <doi:10.1016/B978-1-55860-332-5.50011-0> and we provide a user friendly graphical interface for setting up such problems via directed acyclic graphs (DAG), which only allow for problems within this class to be depicted. The user can then define linear constraints to further refine their assumptions to meet their specific problem, and then specify a causal query using a text interface. The program converts this user defined DAG, query, and constraints, and returns tight bounds. The bounds can be converted to R functions to evaluate them for specific datasets, and to latex code for publication. The methods and proofs of tightness and validity of the bounds are described in a paper by Sachs, Jonzon, Gabriel, and Sjölander (2022) <doi:10.1080/10618600.2022.2071905>.

Maintained by Michael C Sachs. Last updated 19 days ago.

1.7 match 16 stars 6.92 score 29 scripts

freezenik

bamlss:Bayesian Additive Models for Location, Scale, and Shape (and Beyond)

Infrastructure for estimating probabilistic distributional regression models in a Bayesian framework. The distribution parameters may capture location, scale, shape, etc. and every parameter may depend on complex additive terms (fixed, random, smooth, spatial, etc.) similar to a generalized additive model. The conceptual and computational framework is introduced in Umlauf, Klein, Zeileis (2019) <doi:10.1080/10618600.2017.1407325> and the R package in Umlauf, Klein, Simon, Zeileis (2021) <doi:10.18637/jss.v100.i04>.

Maintained by Nikolaus Umlauf. Last updated 5 months ago.

openblas

2.0 match 1 stars 5.76 score 239 scripts 5 dependents

pbs-software

PBSmodelling:GUI Tools Made Easy: Interact with Models and Explore Data

Provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface ('GUI'). Although our simplified 'GUI' language depends heavily on the R interface to the 'Tcl/Tk' package, a user does not need to know 'Tcl/Tk'. Examples illustrate models built with other R packages, including 'PBSmapping', 'PBSddesolve', and 'BRugs'. A complete user's guide 'PBSmodelling-UG.pdf' shows how to use this package effectively.

Maintained by Rowan Haigh. Last updated 4 months ago.

1.7 match 2 stars 6.76 score 120 scripts 4 dependents