UCSCXenaShiny (version 2.1.0)

vis_toil_Mut: Visualize molecular profile difference between mutation and wild status of queried gene

Description

Visualize molecular profile difference between mutation and wild status of queried gene

Usage

vis_toil_Mut(
  mut_Gene = "TP53",
  Gene = NULL,
  data_type = NULL,
  Mode = c("Boxplot", "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,
  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

opt_pancan

specify one dataset for some molercular profiles

Examples

if (FALSE) {
p <- vis_toil_Mut(mut_Gene = "TP53")
p <- vis_toil_Mut(mut_Gene = "TP53", Gene = "TNF")
p <- vis_toil_Mut(mut_Gene = "TP53", Gene = "hsa-let-7d-3p", data_type = "miRNA")
}