| plot.referenceComparison {cTRAP} | R Documentation |
Plot data comparison
## S3 method for class 'referenceComparison'
plot(x, method = c("spearman", "pearson",
"gsea", "rankProduct"), n = c(3, 3), showMetadata = TRUE,
plotNonRankedPerturbations = FALSE, alpha = 0.3, ...)
x |
|
method |
Character: method to plot results ( |
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 |
Plot illustrating the reference comparison
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
# 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")