vis_toil_Mut_cancer: Visualize molecular profile difference between mutation and...

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

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
)

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

Value

a ggplot object or a tibble data.frame.

UCSCXenaShiny documentation built on May 29, 2024, 1:10 a.m.