Summary of CNV statuses in bar plots

Source: R/CNV.R

Provides the summary of CNV statuses of EIF4F genes in tumors from all TCGA cancer types combined and in tumors from individual TCGA cancer types

.plot_bargraph_CNV_TCGA(gene_list)

Arguments

gene_list

gene names in a vector of characters

Details

This function

  • selects a subset of CNV and sample type data of only EIF4F gene from the data frame TCGA_CNV_sampletype - a global variable generated from initialize_cnv_data().

  • uses the subset data .TCGA_CNV_sampletype_subset to perform the CNV status analysis of all inquired genes with the internal functions .CNV_all_cancer() and plot the results as a bar plot with the internal function .CNV_sum_barplot().

  • uses the same subset data .TCGA_CNV_sampletype_subset to perform CNV status analysis for each gene across all tumors types by the internal function .CNV_ind_cancer() and plots the CNV results by the internal function .CNV_barplot().

This function is not accessible to the user and will not show at the users' workspace. It can only be called by the exported EIF4F_CNV_analysis() function.

Side effects:

(1) the stacked bar plots on screen and as pdf files to show the summary table of the CNV statuses of all gene_list in TCGA tumors

(2) stacked bar plots on screen and as saved pdf files to show CNV status of each gene in gene_list from an individual cancer type

See also

Other composite function to call CNV data analysis and plotting: .plot_boxgraph_CNVratio_TCGA()

Examples

if (FALSE) {
plot_bargraph_CNV_TCGA(c(
  "TP53", "EIF4A1", "EIF4A2", "EIF4E",
  "EIF4E2", "EIF4E3", "MYC", "EIF3D", "EIF4EBP1", "EIF4G1", "EIF4G2",
  "EIF4G3", "PABPC1", "MKNK1", "MKNK2"
))
}