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Plot the separation of reference genes

Source: R/reference_genes.R
plot_reference_separation.Rd

Plots the distribution of the scores (by default the log2 fold changes) of the essential and non-essential reference genes, with the quality metrics of compute_screen_quality in the subtitle. In a good dropout screen the two distributions are well separated and the essential genes are on the left.

Usage

plot_reference_separation(
  table,
  essential,
  nonessential,
  score = "Log2FC",
  level = c("gene", "barcode"),
  alpha = 0.5
)

Arguments

table

A table with one row for each barcode and the columns Gene and score, for example the output of compute_metrics or compute_barcode_statistics.

essential

The names of the essential genes (as in the Gene column).

nonessential

The names of the non-essential genes.

score

The column with the score (default "Log2FC").

level

"gene" (default) to average the scores of the barcodes of each gene, or "barcode" to use each barcode.

alpha

The transparency of the densities.

Value

A ggplot object.

See also

compute_screen_quality

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
metrics <- compute_metrics(object,
    control = "TRT", treatment = "Time3", day = "Time3"
)
# Example only: two arbitrary sets of genes used as references
genes <- unique(as.character(metrics$Gene))
plot_reference_separation(metrics,
    essential = genes[1:20], nonessential = genes[21:60]
)