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]