Plot gene effect vs. expression

plotGeneEffectVsExpression(effect, expression, ...)

# S4 method for GeneEffect,CCLEExpressionData
plotGeneEffectVsExpression(
  effect,
  expression,
  gene,
  subtype = NULL,
  subtypeCol = "subtype",
  label = !is.null(FALSE)
)

Arguments

effect	`GeneEffect`.
expression	`CCLEExpressionData`.
...	Additional arguments.
gene	`character(1)`. Gene identifier.
subtype	`character(1)` or `NULL`. Cell subtype name to use for filtering.
subtypeCol	`character(1)`. Column name of metadata defined in `colData` of `effect`.
label	`logical(1)`. Superimpose sample text labels on the plot.

Note

Updated 2021-07-15.

Examples

data(crispr)

effect <- crispr
expression <- CCLEExpressionData()
#> → Downloading DepMap file <https://ndownloader.figshare.com/files/27902091>.
#> → Importing /Users/mike/.cache/R/DepMapAnalysis/f54038b7a977_27902091 using data.table::`fread()`.
#> → Downloading Homo sapiens gene info from NCBI at <ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz>.
#> → Importing /Users/mike/.cache/R/AcidGenomes/50321924c0cb_Homo_sapiens.gene_info.gz using data.table::`fread()`.
#> ! 3 retired NCBI Entrez identifiers in data set: BCAR3_723788, MICAL2_84953, USP4_107986084.
#> → Downloading DepMap file <https://ndownloader.figshare.com/files/27902376>.
#> → Importing /Users/mike/.cache/R/DepMapAnalysis/66871289d630_27902376 using data.table::`fread()`.
#> ! 1 missing cell line in `colData`: ACH_001316.

## GeneEffect,CCLEExpressionData ====
gene <- rownames(effect)[[1L]]
plotGeneEffectVsExpression(
    effect = effect,
    expression = expression,
    gene = gene
)
#> Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider increasing max.overlaps