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Plot the empirical null of the gene statistics

Source: R/empirical_null.R
plot_empirical_null.Rd

Plots the distribution of the gene statistics used by find_gene_zscore_hit with reference = "empirical", together with the fitted null (scaled to the share of genes it describes). The null should follow the centre of the distribution; the hits are in the tail on the side of direction.

Usage

plot_empirical_null(
  table_treate_vs_control,
  score = c("Zscore", "ZscoreRobust"),
  direction = c("Down", "Up"),
  statistic = c("mean", "median"),
  min_barcodes = 3,
  empirical_fit = c("central", "one-sided"),
  bins = 60
)

Arguments

table_treate_vs_control

A table with one row for each barcode and at least the columns Gene, Log2FC and the score column, as returned by compute_metrics or compute_barcode_statistics.

score

The column to use as score: "Zscore" (default) or "ZscoreRobust".

direction

"Down" (default) or "Up".

statistic

The gene score: "mean" (default) or "median".

min_barcodes

Genes with fewer barcodes than this are not used (default 3).

empirical_fit

"central" (default) or "one-sided".

bins

The number of bins of the histogram. Default 60.

Value

A ggplot object.

See also

find_gene_zscore_hit

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
table <- compute_metrics(object,
    control = "Time3", treatment = "TRT",
    day = "Time3"
)
plot_empirical_null(table)