# Visualization Of Differential Expression Analysis

## 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