plotTargetingDrugsVSsimilarPerturbations: Plot similar perturbations against predicted targeting drugs

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Plot similar perturbations against predicted targeting drugs

Description

Plot similar perturbations against predicted targeting drugs

Usage

plotTargetingDrugsVSsimilarPerturbations(
  targetingDrugs,
  similarPerturbations,
  column,
  labelBy = "pert_iname",
  quantileThreshold = 0.25,
  showAllScores = FALSE,
  keyColTargetingDrugs = NULL,
  keyColSimilarPerturbations = NULL
)

Arguments

targetingDrugs	targetingDrugs object
similarPerturbations	similarPerturbations object
column	Character: column to plot (must be available in both databases)
labelBy	Character: column in as.table(similarPerturbations) or as.table(targetingDrugs) to be used for labelling
quantileThreshold	Numeric: quantile (between 0 and 1) to highlight values of interest
showAllScores	Boolean: show all scores? If FALSE, only the best score per compound will be plotted
keyColTargetingDrugs	Character: column from targetingDrugs to compare with column keyColSimilarPerturbations from similarPerturbations; automatically selected if NULL
keyColSimilarPerturbations	Character: column from similarPerturbations to compare with column keyColTargetingDrugs from targetingDrugs; automatically selected if NULL

Value

ggplot2 plot

See Also

Other functions related with the ranking of CMap perturbations: as.table.referenceComparison(), filterCMapMetadata(), getCMapConditions(), getCMapPerturbationTypes(), loadCMapData(), loadCMapZscores(), parseCMapID(), plot.perturbationChanges(), plot.referenceComparison(), prepareCMapPerturbations(), print.similarPerturbations(), rankSimilarPerturbations()

Other functions related with the prediction of targeting drugs: as.table.referenceComparison(), listExpressionDrugSensitivityAssociation(), loadExpressionDrugSensitivityAssociation(), plot.referenceComparison(), predictTargetingDrugs()

Examples

# Rank similarity against CMap compound perturbations
similarPerts <- rankSimilarPerturbations(diffExprStat,
                                         cmapPerturbationsCompounds)

# Predict targeting drugs
gdsc <- loadExpressionDrugSensitivityAssociation("GDSC 7")
predicted <- predictTargetingDrugs(diffExprStat, gdsc)

plotTargetingDrugsVSsimilarPerturbations(predicted, similarPerts,
                                         "spearman_rank")

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.