Visualize Pan-cancer TPM (tumor (TCGA) vs Normal (TCGA & GTEx))

Usage

vis_toil_TvsN(
  Gene = "TP53",
  Mode = c("Boxplot", "Violinplot"),
  data_type = "mRNA",
  Show.P.value = TRUE,
  Show.P.label = TRUE,
  Method = c("wilcox.test", "t.test"),
  values = c("#DF2020", "#DDDF21"),
  TCGA.only = FALSE,
  draw_quantiles = c(0.25, 0.5, 0.75),
  trim = TRUE,
  include.Tumor.only = FALSE,
  opt_pancan = .opt_pancan
)

Arguments

Gene: a molecular identifier (e.g., "TP53") or a formula specifying genomic signature ("TP53 + 2 * KRAS - 1.3 * PTEN").
Mode: "Boxplot" or "Violinplot" to represent data
data_type: choose gene profile type, including "mRNA", "transcript", "protein", "mutation", "cnv", "methylation", "miRNA".
Show.P.value: TRUE or FALSE whether to count P value
Show.P.label: TRUE or FALSE present p value with number or label *, **, *** and ****
Method: default method is wilcox.test
values: the color to fill tumor or normal
TCGA.only: include samples only from TCGA dataset
draw_quantiles: draw quantiles for violinplot
trim: whether trim the violin
include.Tumor.only: if TRUE, include "UVM" and "MESO" these two types with matched normals samples.
opt_pancan: specify one dataset for some molercular profiles

Value

a ggplot object

Examples

if (FALSE) {
p <- vis_toil_TvsN(Gene = "TP53", Mode = "Violinplot", Show.P.value = FALSE, Show.P.label = FALSE)
p <- vis_toil_TvsN(Gene = "TP53", Mode = "Boxplot", Show.P.value = FALSE, Show.P.label = FALSE)
}