plot_rates_clon_excl: Barplot of rates of clonal exclusivity and number of clones.

In GeneAccord: Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Description

This function plots the average rates of clonal exclusivity for each patient.

Usage

plot_rates_clon_excl(avg_rates_m, clone_tbl, output_pdf = "direct")

Arguments

avg_rates_m	A named vector with the average rates of clonal exclusivity for each patient. The name of each element is the patient id to be used in the barplot.
clone_tbl	The tibble containing the gene-to-clone assignments from all patients and all trees from the collection of trees.
output_pdf	The name of the pdf to be generated. Or if output_pdf is "direct", then the plot is generated directly and not to a pdf. Default: "direct"

Details

In addition to the average rate of clonal exclusivity, it also visualizes the average number of clones of each patient.

Value

None, the function plots the average rates of clonal exclusivity.

Author(s)

Ariane L. Moore

Examples

clone_tbl <- dplyr::tibble(
            "file_name"=rep(c(rep(c("fn1", "fn2"), each=3)), 2),
            "patient_id"=rep(c(rep(c("pat1", "pat2"), each=3)), 2),
            "altered_entity"=c(rep(c("geneA", "geneB", "geneC"), 4)),
            "clone1"=c(0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0),
            "clone2"=c(1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 0, 1),
            "tree_id"=c(rep(1, 6), rep(2, 6)))
avg_rates_m <- c(pat1=0.014, pat2=0.3)
plot_rates_clon_excl(avg_rates_m, clone_tbl)

GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.