plot.perturbationChanges {cTRAP}R Documentation

Plot perturbation comparison against a differential expression profile

Description

Plot perturbation comparison against a differential expression profile

Usage

## S3 method for class 'perturbationChanges'
plot(x, perturbation, diffExprGenes,
  method = c("spearman", "pearson", "gsea"), geneSize = 150,
  genes = c("both", "top", "bottom"), ...)

Arguments

x

perturbationChanges object

perturbation

Character (perturbation identifier) or a similarPerturbations table (from which the respective perturbation identifiers are retrieved)

diffExprGenes

Numeric: named vector of differentially expressed genes whose names are gene identifiers and respective values are a statistic that represents significance and magnitude of differentially expressed genes (e.g. t-statistics)

method

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

geneSize

Number: top and bottom number of differentially expressed genes for gene set enrichment (only used if method = gsea)

genes

Character: when plotting gene set enrichment analysis (GSEA), plot top genes (genes = "top"), bottom genes (genes = "bottom") or both (genes = "both"); only used if method = "gsea"

...

Extra arguments (currently undocumented)

Value

CMap data comparison plots

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.referenceComparison, plotTargetingDrugsVSsimilarPerturbations, prepareCMapPerturbations, print.similarPerturbations, rankSimilarPerturbations

Examples

data("diffExprStat")
data("cmapPerturbationsKD")

compareKD <- rankSimilarPerturbations(diffExprStat, cmapPerturbationsKD)
EIF4G1knockdown <- grep("EIF4G1", compareKD[[1]], value=TRUE)
plot(cmapPerturbationsKD, EIF4G1knockdown, diffExprStat, method="spearman")
plot(cmapPerturbationsKD, EIF4G1knockdown, diffExprStat, method="pearson")
plot(cmapPerturbationsKD, EIF4G1knockdown, diffExprStat, method="gsea")

data("cmapPerturbationsCompounds")
pert <- "CVD001_HEPG2_24H:BRD-A14014306-001-01-1:4.1"
plot(cmapPerturbationsCompounds, pert, diffExprStat, method="spearman")
plot(cmapPerturbationsCompounds, pert, diffExprStat, method="pearson")
plot(cmapPerturbationsCompounds, pert, diffExprStat, method="gsea")

# Multiple cell line perturbations
pert <- "CVD001_24H:BRD-A14014306-001-01-1:4.1"
plot(cmapPerturbationsCompounds, pert, diffExprStat, method="spearman")
plot(cmapPerturbationsCompounds, pert, diffExprStat, method="pearson")

# Currently unsupported!
# plot(cmapPerturbationsCompounds, pert, diffExprStat, method="gsea")
[Package cTRAP version 1.5.0 Index]