Visualization Of Differential Expression Analysis

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Documentation for package ‘daVis’ version 0.99.4

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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