plot.perturbationChanges {cTRAP} | R Documentation |
Plot perturbation comparison against a differential expression profile
## S3 method for class 'perturbationChanges' plot(x, perturbation, diffExprGenes, method = c("spearman", "pearson", "gsea"), geneSize = 150, genes = c("both", "top", "bottom"), ...)
x |
|
perturbation |
Character (perturbation identifier) or a
|
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 ( |
geneSize |
Number: top and bottom number of differentially expressed
genes for gene set enrichment (only used if |
genes |
Character: when plotting gene set enrichment analysis (GSEA),
plot top genes ( |
... |
Extra arguments (currently undocumented) |
CMap data comparison plots
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
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")