plot.referenceComparison {cTRAP}R Documentation

Plot data comparison

Description

Plot data comparison

Usage

## S3 method for class 'referenceComparison'
plot(x, method = c("spearman", "pearson",
  "gsea", "rankProduct"), n = c(3, 3), showMetadata = TRUE,
  plotNonRankedPerturbations = FALSE, alpha = 0.3, ...)

Arguments

x

referenceComparison object: obtained after running rankSimilarPerturbations or predictTargetingDrugs

method

Character: method to plot results (spearman, pearson, gsea or rankProduct)

n

Numeric: number of top and bottom genes to label (if a vector of two numbers is given, the first and second numbers will be used as the number of top and bottom genes to label, respectively)

showMetadata

Boolean: show available metadata information instead of identifiers (if available)?

plotNonRankedPerturbations

Boolean: plot non-ranked data in grey?

alpha

Numeric: transparency

...

Extra arguments currently not used

Value

Plot illustrating the reference comparison

See Also

Other functions related with the ranking of CMap perturbations: [.perturbationChanges, as.table.similarPerturbations, dim.perturbationChanges, dimnames.perturbationChanges, filterCMapMetadata, getCMapConditions, getCMapPerturbationTypes, loadCMapData, loadCMapZscores, parseCMapID, plot.perturbationChanges, plotTargetingDrugsVSsimilarPerturbations, prepareCMapPerturbations, print.similarPerturbations, rankSimilarPerturbations

Other functions related with the prediction of targeting drugs: loadExpressionDrugSensitivityAssociation, plotTargetingDrugsVSsimilarPerturbations, predictTargetingDrugs

Examples

# Example of a differential expression profile
data("diffExprStat")

## Not run: 
# Download and load CMap perturbations to compare with
cellLine <- "HepG2"
cmapMetadataKD <- filterCMapMetadata(
  "cmapMetadata.txt", cellLine=cellLine,
  perturbationType="Consensus signature from shRNAs targeting the same gene")

cmapPerturbationsKD <- prepareCMapPerturbations(
  cmapMetadataKD, "cmapZscores.gctx", "cmapGeneInfo.txt", loadZscores=TRUE)

## End(Not run)

# Rank similar CMap perturbations
compareKD <- rankSimilarPerturbations(diffExprStat, cmapPerturbationsKD)

plot(compareKD, "spearman", c(7, 3))
plot(compareKD, "pearson")
plot(compareKD, "gsea")

[Package cTRAP version 1.4.0 Index]