Package: daVis 0.99.4

Katarzyna Gorczak

daVis: Visualization Of Differential Expression Analysis

This package contains utility functions to visualize the output from differential expression analysis. The input can be either a model or a list of top tables or a combination of the two. The model can be output from limma, edgeR or DESeq2.

Authors:Katarzyna Gorczak [aut, cre], Laure Cougnaud [aut]

daVis_0.99.4.tar.gz
daVis_0.99.4.zip(r-4.7)daVis_0.99.4.zip(r-4.6)daVis_0.99.4.zip(r-4.5)
daVis_0.99.4.tgz(r-4.6-any)daVis_0.99.4.tgz(r-4.5-any)
daVis_0.99.4.tar.gz(r-4.7-any)daVis_0.99.4.tar.gz(r-4.6-any)
daVis_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
daVis/json (API)

# Install 'daVis' in R:

install.packages('daVis', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/openanalytics/davis/issues

On BioConductor:daVis-0.99.3(bioc 3.24)

visualization datarepresentation differentialexpression software microarray rnaseq

4.40 score 4 scripts 10 exports 54 dependencies

Last updated from:5f2212fe2f. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	211
linux-devel-x86_64	OK	458
source / vignettes	OK	337
linux-release-x86_64	OK	504
macos-release-arm64	OK	370
macos-oldrel-arm64	OK	360
windows-devel	OK	414
windows-release	OK	406
windows-oldrel	OK	404
wasm-release	OK	171

Exports:createExampleData daHeatmapLogFC daLogRatioPlot daMAplot daScatterPlot daSignificantGenesBarplot daUpset daVolcanoPlot daWaterfallPlot getSEModel

Dependencies:abind BH Biobase BiocGenerics BiocParallel cli codetools cpp11 DelayedArray DESeq2 edgeR farver formatR futile.logger futile.options generics GenomicRanges ggh4x ggplot2 glue gridExtra gtable IRanges isoband labeling lambda.r lattice legendry lifecycle limma locfit Matrix MatrixGenerics matrixStats plyr R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod SummarizedExperiment UpSetR vctrs viridisLite withr XVector

daVis

Rendered fromdaVis-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-05-08
Started: 2026-01-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add column with hover text to top table	addHoverText
Arrange top tables	arrangeTopTables
Calculate correlation	calcCorrelation
Create ggplot object with barplot	callBarplot
Create ggplot object with heatmap	callHeatmap
Create ggplot object with log ratio plot	callLogRatioPlot
Create ggplot object with MA plot	callMAplot
Create ggplot object with scatter plot	callScatterPlot
Create ggplot object with volcano plot	callVolcanoPlot
Create ggplot object with waterfall plot	callWaterfallPlot
Combine data.frames by columns allowing for different number of rows.	cbindFill
Check coefficients	checkCoef
Check input fields	checkColumns
Check input	checkInput
Color-blind palette	colorBlindPalette
Concatenate feature variables	concatenateVars
Create table for barplot	createDataBarplot
Create table for heatmap	createDataHeatmap
Create table for log ratio plot	createDataLogRatioPlot
Create table for MA plot	createDataMAplot
Create table for the scatter plot	createDataScatterPlot
Create data for upset plot	createDataUpsetPlot
Create table for the volcano plot	createDataVolcanoPlot
Create data for waterfall plot	createDataWaterfallPlot
Create example limma-, edgeR-object or a list of top tables.	createExampleData
Create ExpressionSet object from example data	createExpressionSet
Create pairwise data	createPairData
Create sample annotation from example data	createSampleAnnotation
Create table for genes of interest	createTopTableGenesOfInterest
Heatmap of log fold-changes	daHeatmapLogFC
Plot log ratios	daLogRatioPlot
MA plot	daMAplot
Scatter plot	daScatterPlot
Barplot with the number of significant genes	daSignificantGenesBarplot
Upset plot for up- or down-regulated genes	daUpset
Common parameters for the functions of the 'daVis' package.	daVis-common-args
Common documentation for the 'daVis' package.	daVis-common-doc
Volcano plot	daVolcanoPlot
Waterfall plot	daWaterfallPlot
Download example data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60450	downloadData
Extract columns of interest from top table	extractColsOfInterest
Extract feature ids for each overlapping set	extractFeatures
Get top table per pair (ref and comp coef) for scatter plot	extractPairs
Extract query list	extractQueryList
Extract top tables for coefficients of interest	extractTopTables
Extract top table for a specific coef	extractTTcoef
Add facets to ggplot object	facet
Filter top tables based on common features across all tables	filterCommonFeatures
Filter genes of interest	filterGenesOfInterest
Filter top tables based on logFC threshold	filterLogFC
Format aesthetics for the main plot with MA plot	formatAesMA
Format aesthetics for the main plot with volcano plot	formatAesVP
Format aesthetics for the main plot with waterfall plot	formatAesWP
extend manual scale values if required	formatManualScale
Format top table for a specific coefficient	formatTTcoef
shorten string length	formatVariableLength
remove space in variable name	formatVariableSpace
Create colors for coefficient labels	getCoefColor
Get coefficient label	getCoefLabel
Create colors for feature labels	getFeatureColor
Get features from input	getFeatures
Get ID of the input 'list' matching to the specific coefficient	getInputIdCoef
Get coefficients in input	getModelCoefs
Get number of significant genes for coefficient	getNumberOfRegulatedGenes
Get number of significant genes for coefficient	getNumberOfSignificantGenes
Get standard error from a limma model.	getSEModel
Get top features	getTopFeatures
Get top genes with highest significance and top genes with highest logFC	getTopGenes
Extract top tables from a model	getTopTableFromModel
Customized ggplot theme	ggPlotTheme
Check if input is a model	isModel
Check if input is a topTable containing colums with logFC, p-value and adjusted p-value	isTopTable
Add label with correlation to scatter plot	labelCorr
Add layer with genes of interest to ggplot object	labelGenesOfInterest
Add optional text to the log-ratio plot	labelTextLRP
Add point labels to ggplot object	labelTopGenes
Create main plot object with heatmap	mainH
Create main plot object with log-ratio plot	mainLRP
Create main plot object with MA plot	mainMA
Create main plot object with scatter plot	mainSP
Create main plot object with volcano plot	mainVP
Create main plot object with waterfall plot	mainWP
Make elements unique	makeElementsUnique
Normalize data, create model matrix and contrasts	modelExampleData
Sort the comparison columns according to the coefficients	orderComparison
Order features based on similarity or significance	orderFeatures
Process table for visualizations.	processFeatures
Reshape table	reshapeTable
Fit the model with DESeq2	runDESeq2
Fit the model with edgeR	runEdgeR
Fit the model with limma	runLimma
Fit the model and return top table	runTopTable
check if variable is not numeric (or integer)	setCategoricalElement
check if the aesthetic is fixed (e.g. color, shape, size 'palette')	setFixElement
check if manual aesthetic for the gradient should be set	setGradientScale
check if manual aesthetic should be set	setManualScale
Subset input with specific features	subsetFeatures
Extract top features from 'DESeq2' output	topFeaturesDeseq
Extract top features from 'edgeR' output	topFeaturesEdger
Extract top features from 'limma' output	topFeaturesLimma