UCSCXenaShiny (version 2.1.0)

vis_toil_Mut_cancer: Visualize molecular profile difference between mutation and wild status of queried gene in Single Cancer Type

Description

Visualize molecular profile difference between mutation and wild status of queried gene in Single Cancer Type

Usage

vis_toil_Mut_cancer(
  mut_Gene = "TP53",
  Gene = NULL,
  data_type = NULL,
  Mode = c("Dotplot", "Violinplot"),
  Show.P.value = TRUE,
  Show.P.label = TRUE,
  Method = c("wilcox.test", "t.test"),
  values = c("#DF2020", "#DDDF21"),
  draw_quantiles = c(0.25, 0.5, 0.75),
  trim = TRUE,
  Cancer = "ACC",
  opt_pancan = .opt_pancan
)

Value

a ggplot object or a tibble data.frame.

Arguments

mut_Gene

the queried gene to determine grouping based on mutation and wild status

Gene

a molecular identifier (e.g., "TP53") or a formula specifying genomic signature ("TP53 + 2 * KRAS - 1.3 * PTEN").

data_type

choose gene profile type, including "mRNA", "transcript", "methylation", "miRNA".

Mode

choose one visualize mode to represent data

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 mutation or wild status

draw_quantiles

draw quantiles for violinplot

trim

whether to trim the violin

Cancer

select cancer cohort(s).

opt_pancan

specify one dataset for some molercular profiles