make_barplot_on_synergy_subset_stats: Bar plot of observed synergy subsets

In emba: Ensemble Boolean Model Biomarker Analysis

Description

Use this function to easily make a barplot that shows the amount of models that predicted each synergy subset out of the set of all observed synergies.

Usage

make_barplot_on_synergy_subset_stats(
  synergy.subset.stats,
  threshold.for.subset.removal,
  bottom.margin,
  ylim.add = 0,
  cell.line = NULL
)

Arguments

synergy.subset.stats	integer vector with values the amount of models that predicted each synergy subset, defined as a comma-separated string of drug combinations in the names attribute of the vector
threshold.for.subset.removal	integer. Use it to discard elements of the synergy.subset.stats vector that are strictly less than the specified threshold
bottom.margin	integer used to vertically fit in the names of the drug combinations in the x-axis (specified in inches). The best bottom.margin value depends on the maximum size of a synergy subset as defined in the names attribute of the synergy.subset.stats. Some rules of thumb are: size = 1 => bottom.margin = 4, size = 2 => bottom.margin = 6, size = 3 => bottom.margin = 9, size = 4 => bottom.margin = 12, etc.
ylim.add	integer. Signifies the height to add to the upper ylim parameter on the barplot, in addition to the maximum bar height across the whole plot. Default value is 0.
cell.line	string. The name of the cell line to be used in the title of the produced plot. Default value: NULL (the cell line name will not be added to the title).

Examples

synergy.subset.stats = c(1,4,3,2)
names(synergy.subset.stats) = c("A-B", "B-C", "C-A", "C-D")
make_barplot_on_synergy_subset_stats(synergy.subset.stats,
threshold.for.subset.removal = 0, bottom.margin = 4, ylim.add = 0.5)

emba documentation built on Jan. 7, 2021, 9:09 a.m.