Showing 200 of total 328 results (show query)
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.
softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap
47.6 match 1.3k stars 16.93 score 16k scripts 151 dependentsstefanedwards
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-linesfacetsggplot-extensionggplot2knitrlegendticksvisualization
30.0 match 190 stars 11.98 score 1.7k scripts 4 dependentsriatelab
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.
cartographymapthematic-mapscpp
19.6 match 399 stars 10.47 score 460 scripts 2 dependentsteunbrand
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.
axisaxis-customizationggplot-extensionggplot2legendvisualization
21.2 match 227 stars 7.83 score 29 scripts 2 dependentstidyverse
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-visualisationvisualisation
6.0 match 6.6k stars 25.10 score 645k scripts 7.5k dependentsdmurdoch
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 dependentsriatelab
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.
21.5 match 13 stars 6.33 score 5 scripts 14 dependentsr-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-mapsmapsspatialthematic-mapsvisualisation
7.4 match 880 stars 16.73 score 13k scripts 24 dependentsjonocarroll
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 dependentstomroh
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.
10.9 match 35 stars 9.46 score 132 scripts 20 dependentsanimint
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 scriptsjfrench
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 dependentschris-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 scriptssymbolixau
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.
deckglgeospatialmapboxmapbox-glmapbox-gl-jsmapscpp
9.0 match 363 stars 10.30 score 368 scripts 1 dependentshgerritsen
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 dependentsms609
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.
15.5 match 5.30 score 6 scripts 16 dependentsplotly
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.
d3jsdata-visualizationggplot2javascriptplotlyshinywebgl
4.1 match 2.6k stars 19.43 score 93k scripts 797 dependentskarlines
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 dependentsjohncoene
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.
echartshacktoberfesthtmlwidgethtmlwidgetsvisualization
6.6 match 603 stars 11.45 score 1.3k scripts 11 dependentswilkelab
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 dependentsmuvisu
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.
8.3 match 7 stars 8.39 score 30 scripts 1 dependentstaiyun
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.
3.9 match 323 stars 17.66 score 28k scripts 517 dependentsdfsp-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.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
10.7 match 66 stars 6.47 score 15 scriptskof-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 scriptsharrelfe
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.
3.9 match 210 stars 17.61 score 17k scripts 750 dependentsthomasp85
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-extensionggplot2graph-visualizationnetwork-visualizationvisualizationcpp
4.0 match 1.1k stars 16.96 score 9.2k scripts 111 dependentsrstudio
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.
3.7 match 821 stars 17.20 score 39k scripts 178 dependentsggobi
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 dependentswalkerke
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 scriptsdreamrs
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.
6.1 match 174 stars 9.74 score 96 scripts 4 dependentsadeverse
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.
3.8 match 39 stars 14.96 score 2.2k scripts 256 dependentsrstudio
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 dependentsbrandmaier
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 scriptsrempsyc
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-functionsggplot2psychologystatisticsvisualization
5.0 match 43 stars 10.68 score 214 scripts 2 dependentsjbengler
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 scriptsbraverock
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 dependentsedzer
hexbin:Hexagonal Binning Routines
Binning and plotting functions for hexagonal bins.
Maintained by Edzer Pebesma. Last updated 4 months ago.
3.8 match 37 stars 14.00 score 2.4k scripts 114 dependentsteunbrand
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.
3.8 match 616 stars 13.98 score 4.4k scripts 20 dependentsdanchaltiel
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-statisticsflextablefrequency-tablehtml-reportmswordofficer
5.0 match 116 stars 10.37 score 340 scriptsdatastorm-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 dependentsusaid-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 scriptsandysouth
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 dependentsgforge
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.
3.9 match 43 stars 11.47 score 716 scripts 21 dependentsmurrayefford
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.
4.3 match 3 stars 10.18 score 410 scripts 5 dependentsjoshuaulrich
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.
2.3 match 221 stars 18.38 score 12k scripts 654 dependentsbioc
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.
visualizationgenomeannotationfunctionalgenomicsgenomeassemblyhiccpp
4.0 match 308 stars 10.16 score 167 scripts 3 dependentsbrry
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 dependentsqile0317
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-analysisimmune-repertoireimmune-systemscrna-seqscrnaseqseuratsingle-cellsingle-cell-genomicscpp
6.1 match 15 stars 6.45 score 15 scriptsjuba
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.
4.3 match 160 stars 8.98 score 125 scripts 4 dependentshadley
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 dependentsmstrimas
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 scriptsuclahs-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 dependentsrspatial
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.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
2.0 match 559 stars 17.64 score 17k scripts 851 dependentsdeepayan
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 dependentsdreamrs
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.
4.0 match 144 stars 8.51 score 247 scriptsmrjoh3
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.
5.3 match 39 stars 6.45 score 72 scriptspalaeoverse
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-rggplot2phylopicsilhouette
3.5 match 91 stars 9.25 score 272 scriptsmages
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 dependentsfunkyheatmap
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 scriptsbioc
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.
4.3 match 7.63 score 94 scripts 5 dependentskcuilla
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.
customizationdata-visualizationeasy-to-usereproducibletables
3.7 match 209 stars 8.79 score 460 scripts 4 dependentsncss-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.
ksslnasisnrcssoilsoil-data-accesssoil-surveysoilwebsqlusda
2.8 match 87 stars 11.34 score 1.0k scripts 1 dependentscran
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 dependentskassambara
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 dependentspik-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 dependentspaulojus
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 dependentsstemangiola
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.
assaydomaininfrastructurebrewercomplexheatmapcustom-palettedplyrgraphvizheatmapmtcarsplottingrstudioscaletibbletidytidy-data-frametidybulktidyverseviridis
3.0 match 335 stars 10.23 score 197 scripts 1 dependentslgnbhl
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.
6.6 match 12 stars 4.48 score 4 scriptssvkucheryavski
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 dependentstkonopka
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.
5.2 match 10 stars 5.35 score 15 scriptsbioc
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.
softwarevisualizationdatarepresentationmultiplecomparisonfunctionalpredictiondimensionreductionbioinformaticsheatmapinteractive-visualizationsorthologsphylogenetic-profileshiny
3.5 match 33 stars 7.77 score 10 scriptsheike
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 dependentsccamlr
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 scriptsr-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.
1.5 match 571 stars 18.27 score 7.2k scripts 137 dependentsbioc
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.
dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport
4.0 match 6.85 score 169 scripts 1 dependentsdavidgohel
ggiraph:Make 'ggplot2' Graphics Interactive
Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Maintained by David Gohel. Last updated 3 months ago.
1.9 match 819 stars 14.39 score 4.1k scripts 34 dependentsmartin-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 dependentstrafficonese
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-visualizationgeospatialleaflet
2.0 match 218 stars 13.27 score 2.5k scripts 25 dependentsddediu
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-medicationselectronic-healthcare-datahadoopmedical-databasesmedication-historiespythonsqlvisualisation
3.8 match 28 stars 7.07 score 47 scripts 1 dependentsjbkunst
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.
highchartshtmlwidgetsshinyshiny-rvisualizationwrapper
1.9 match 725 stars 13.93 score 4.9k scripts 18 dependentscran
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 dependentsriatelab
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.
cartographymapspatialspatial-analysis
2.3 match 228 stars 11.28 score 414 scripts 11 dependentsyulab-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-breakcut-plotggbreakggplot2wrap-plot
2.6 match 137 stars 9.81 score 956 scripts 1 dependentssmin95
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-useggplot2scientific-visualizationvisualization
3.5 match 24 stars 7.08 score 288 scripts 1 dependentshta-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 scriptspepijn-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.
3.5 match 15 stars 7.09 score 59 scriptstrevorld
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 dependentsbioc
destiny:Creates diffusion maps
Create and plot diffusion maps.
Maintained by Philipp Angerer. Last updated 4 months ago.
cellbiologycellbasedassaysclusteringsoftwarevisualizationdiffusion-mapsdimensionality-reductioncpp
2.3 match 81 stars 10.94 score 792 scriptsjaimemosg
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-samplingmaximum-likelihood-estimationttt-plot
4.0 match 4 stars 6.07 score 97 scripts 1 dependentsspatstat
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-objectsdistance-calculationgeometrygeometry-processingimagesmensurationplottingpoint-patternsspatial-dataspatial-data-analysis
2.0 match 7 stars 12.11 score 241 scripts 227 dependentsusaid-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 dependentsmilesmcbain
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 scriptsbaptiste
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 dependentsbioc
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.
visualizationsequencinggeneticvariabilitygenomicvariationcoverage
5.5 match 4.30 score 9 scriptscran
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 scoregrantmcdermott
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 dependentscrazycapivara
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-glhtmlwidgetsmapbox-glmapsrspatialspatialwebgl
3.6 match 94 stars 6.40 score 54 scriptsbioc
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.
1.9 match 111 stars 12.26 score 734 scripts 17 dependentslazappi
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.
clusteringclustering-treesvisualisationvisualization
2.0 match 219 stars 11.40 score 1.9k scripts 5 dependentsr4ss
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.
fisheriesfisheries-stock-assessmentstock-synthesis
2.0 match 43 stars 11.38 score 1.0k scripts 2 dependentswilkox
treemapify:Draw Treemaps in 'ggplot2'
Provides 'ggplot2' geoms for drawing treemaps.
Maintained by David Wilkins. Last updated 9 months ago.
data-visualisationggplot2treemap
1.8 match 215 stars 12.58 score 1.6k scripts 9 dependentsmaliny12
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.
3.2 match 11 stars 6.68 score 7 scriptsbioc
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.
immunooncologysoftwaresinglecellonechanneltwochannelmultiplecomparisonnormalizationdataimportbioimagingimaging-mass-cytometrysingle-cellspatial-analysis
2.2 match 32 stars 9.61 score 354 scripts 5 dependentspharmaverse
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 dependentschrislou-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 scriptscran
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 dependentspachadotdev
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.
3.3 match 43 stars 6.31 score 24 scriptsinsee-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 scriptsrhenkin
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.
7.7 match 1 stars 2.70 score 7 scriptslbb220
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 scriptsjvg0mes
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 scorekarlines
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 dependentsbioc
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.
immunooncologyflowcytometrycellbasedassaysinfrastructurevisualization
1.8 match 58 stars 11.25 score 362 scripts 5 dependentscran
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 dependentsrolkra
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-explorationdata-visualisationdecision-treesedarmarkdownshinytidy
1.7 match 228 stars 11.43 score 221 scripts 1 dependentsbioc
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.
immunooncologyproteomicsmassspectrometryclassificationclusteringqualitycontrolbioconductorproteomics-dataspatial-proteomicsvisualisationopenblascpp
2.3 match 15 stars 8.71 score 101 scripts 2 dependentsdavidhodge931
ggblanket:Simplify 'ggplot2' Visualisation
Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Maintained by David Hodge. Last updated 6 days ago.
data-visualisationdata-visualizationggplotggplot-extensionggplot2ggplot2-enhancementsvisualisationvisualization
2.3 match 170 stars 8.43 score 45 scriptscran
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.
4.3 match 2 stars 4.51 score 5 dependentsropensci
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-sciencedrakehigh-performance-computingmakefilepeer-reviewedpipelinereproducibilityreproducible-researchropensciworkflow
1.7 match 1.3k stars 11.49 score 1.7k scripts 1 dependentstconwell
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 dependentsantoineguillot2
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.
d3jsd3partitionrdata-visualizationr-shiny
4.3 match 40 stars 4.30 score 8 scriptsfederico-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 scriptshms-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.
gehlenborglabggplot2upsetupsetrvisualization
1.2 match 781 stars 15.33 score 4.8k scripts 42 dependentskleebaum
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 scriptsbioc
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.
softwarevisualizationsequencing
2.2 match 39 stars 8.24 score 37 scripts 1 dependentsreconhub
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.
1.5 match 58 stars 12.06 score 504 scripts 11 dependentsbioc
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.
microarraytwochannelpreprocessing
2.0 match 8.92 score 222 scripts 37 dependentsalexym1
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 scriptsrmaia
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 dependentssamuel-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.
customizationggplot2scrna-seqseuratsingle-cellsingle-cell-genomicssingle-cell-rna-seqvisualization
2.0 match 242 stars 8.75 score 1.1k scriptssahirbhatnagar
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-riskscox-regressionregression-modelssurvival-analysis
2.4 match 9 stars 7.16 score 94 scriptshrbrmstr
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-visualizationdatavisualizationvega-litevega-lite-specvisualizationwidget
2.3 match 158 stars 7.60 score 84 scriptsthej022214
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 dependentsjessicaweiss
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 scriptstongzhou2017
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.
bioinformaticsitolvisualization
2.3 match 167 stars 7.48 score 60 scriptsmatthewkling
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 scriptsdardisco
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 dependentsacorg
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.
2.0 match 21 stars 8.06 score 362 scriptsepiforecasts
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 dependentsmindthegap-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-modelgeochronologysedimentologystratigraphy
2.3 match 4 stars 7.01 score 34 scripts 1 dependentsadeverse
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 dependentsips-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 dependentsjokergoo
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 dependentsstla
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.
3.3 match 28 stars 4.61 score 29 scriptstimelyportfolio
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.
chartd3htmlwidgetsinteractivejavascriptvisualization
1.5 match 210 stars 10.02 score 310 scripts 4 dependentsjohnxhobbs
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 scriptsn8thangreen
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.
1.5 match 3 stars 9.90 score 243 scripts 3 dependentstraminer
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.
1.8 match 11 stars 8.24 score 534 scripts 13 dependentssymbolixau
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-mapgoogle-mapsgoogle-maps-apigoogle-maps-javascript-apispatialspatial-analysis
1.5 match 236 stars 9.67 score 536 scripts 2 dependentsdatastorm-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 dependentsnvelden
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.
2.4 match 69 stars 5.99 score 13 scriptscran
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 dependentsyunuuuu
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-heatmapsdendrogramdendrogram-heatmapggplotggplot-extensionggplot2heatmapheatmap-visualizationheatmapsmarginal-plotsoncoplotoncoprinttanglegramupsetupsetplot
2.0 match 267 stars 7.08 score 27 scriptsbioc
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.
rnaseqgeneexpressiontranscriptiondifferentialexpressionimmunooncology
1.2 match 422 stars 11.68 score 2.7k scriptsblue-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.
1.8 match 8 stars 7.69 score 163 scripts 3 dependentsmnbram
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 dependentsdreamrs
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 scriptscran
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 scoreteunbrand
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-extensionggplot2ggplot2-geom
1.9 match 54 stars 7.17 score 61 scripts 1 dependentsopenanalytics
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 scriptsrudeboybert
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.
2.0 match 31 stars 6.68 score 146 scriptssyncrosim
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 scriptsegenn
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-sciencedata-visualizationmachine-learningmachine-learning-libraryvisualization
1.9 match 145 stars 7.09 score 50 scripts 2 dependentsmaressyl
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 scriptsbioc
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.
geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk
3.1 match 4.30 score 8 scriptsjamesliley
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 scriptsasa12138
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 dependentsbioc
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.
guidatarepresentationnetworkmultiplecomparisonpathwaysreactomevisualizationgeneexpressiongenetargetanalysisbiocancer-interfacecancercancer-studiesrmarkdown
2.2 match 20 stars 5.95 score 7 scriptsjonathanlees
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 dependentsbioc
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.
1.5 match 8.71 score 145 scripts 2 dependentsbioc
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.
singlecellsoftwaretranscriptomicsrnaseqtranscriptionbiologicalquestiondimensionreductionimmunooncology
2.0 match 24 stars 6.52 score 46 scriptsusccana
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-visualizationigraphnetscinetwork-analysisnetwork-visualizationsnastatnet
1.9 match 51 stars 6.90 score 78 scriptsrishvish
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 dependentsadrientaudiere
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.
sequencingmicrobiomemetagenomicsclusteringclassificationvisualizationampliconamplicon-sequencingbiodiversity-informaticsecologyilluminametabarcodingngs-analysis
2.0 match 17 stars 6.44 score 23 scriptsropensci
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.
abvdafboatlasautotypebivaltypclldglottolog-databaselinguistic-mapslinguisticsphoiblesailstypologywals
1.3 match 51 stars 9.58 score 694 scriptsvinhdizzo
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 scriptsbioc
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.
genesetenrichmentnetworkpathwaysreactomernaseqnetworkenrichmentbioinformaticsnetworkspathway-enrichment-analysisvisualization
1.9 match 26 stars 6.62 score 2 scriptsswarchal
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.
2.0 match 54 stars 6.20 score 146 scriptstoxpi
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-sciencemodelingtoxicology
1.9 match 11 stars 6.58 score 19 scriptsmazamascience
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 scriptsbioc
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.
rnaseqatacseqgeneexpressiontranscriptionsinglecellprincipalcomponentcpp
1.1 match 343 stars 11.12 score 832 scripts 2 dependentsrnabioco
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.
ggplot2ggplot2-geomvisualization
2.0 match 15 stars 6.06 score 38 scriptscran
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.
4.3 match 2.85 scorebioc
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.
guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology
1.8 match 6.65 score 107 scripts 7 dependentsrte-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.
adequacybilandygraphselectricenergyleafletlinear-programmingmanipulatewidgemonte-carlo-simulationoptimizationplotlyprevisionnelrenewable-energyrteshinyshiny-appssimulationstochastic-simulation-algorithmtyndp
1.8 match 21 stars 6.83 score 32 scriptsdfriend21
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.
1.9 match 19 stars 6.34 score 58 scriptspredictiveecology
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.
1.5 match 6 stars 7.92 score 121 scripts 12 dependentsfreezenik
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.
2.0 match 1 stars 5.76 score 239 scripts 5 dependentspbs-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