dot-plot_boxgraph_RNAratio_TCGA: Compare the RNA ratios between EIF4F genes

In a3609640/eIF4F.analysis: A R package to analyze eIF4F subunits in human cancers

Compare the RNA ratios between EIF4F genes

Description

This function generates box plots to compare the RNA ratios between EIF4F genes in tumors tumors vs adjacent normal tissues across TCGA cancer types, and a violin plot to compare RNA ratios in primary, metastatic tumors vs adjacent normal tissues from all TCGA cancer types combined.

Usage

.plot_boxgraph_RNAratio_TCGA(
  gene01,
  gene02,
  gene03,
  gene04,
  gene05,
  gene06,
  gene07,
  gene08,
  gene09,
  gene10
)

Arguments

gene01	gene name as a string
gene02	gene name as a string
gene03	gene name as a string
gene04	gene name as a string
gene05	gene name as a string
gene06	gene name as a string
gene07	gene name as a string
gene08	gene name as a string
gene09	gene name as a string
gene10	gene name as a string

Details

This function

• calculates RNA ratio across individual tumor types from all cancers with the function .RNAratio_calculation(),

• selects the ratio data with .RNAratio_selection() and make boxplot with .RNAratio_boxplot().

• compares RNA ratio in primary, metastatic tumors vs adjacent normal tissues from all TCGA cancer types combined with the function .RNAratio_tumortype() and plots with .violinplot().

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_DEG_analysis() function.

Side effects:

(1) box plots on screen and as pdf file to show differential RNA ratios in tumors vs NATs in TCGA cancer type

(2) violin plots on screen and as pdf file to show differential gene ratios in primary, metastatic tumors vs adjacent normal tissues from all combined TCGA cancer types

Examples

## Not run: 
.plot_boxgraph_RNAratio_TCGA(
  EIF4E = "EIF4E", EIF4E2 = "EIF4E2",
  EIF4E3 = "EIF4E3", EIF4EBP1 = "EIF4EBP1", EIF4G1 = "EIF4G1", EIF4G2 = "EIF4G2",
  EIF4G3 = "EIF4G3", EIF3D = "EIF3D", EIF4A1 = "EIF4A1", EIF4A2 = "EIF4A2"
)

## End(Not run)

a3609640/eIF4F.analysis documentation built on Jan. 2, 2023, 11:19 p.m.