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")