UCSCXenaShiny (version 2.1.0)

vis_toil_TvsN_cancer: Visualize Gene TPM in Single Cancer Type (Tumor (TCGA) vs Normal (TCGA & GTEx))

Description

Visualize Gene TPM in Single Cancer Type (Tumor (TCGA) vs Normal (TCGA & GTEx))

Usage

vis_toil_TvsN_cancer(
  Gene = "TP53",
  Mode = c("Violinplot", "Dotplot"),
  data_type = "mRNA",
  Show.P.value = FALSE,
  Show.P.label = FALSE,
  Method = "wilcox.test",
  values = c("#DF2020", "#DDDF21"),
  TCGA.only = FALSE,
  Cancer = "ACC",
  opt_pancan = .opt_pancan
)

Value

a ggplot object.

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

Cancer

select cancer cohort(s).

opt_pancan

specify one dataset for some molercular profiles