vis_pcawg_dist: Visualize molecular profile in PCAWG

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

Visualize molecular profile in PCAWG

Description

Visualize molecular profile in PCAWG

Usage

vis_pcawg_dist(
  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"),
  draw_quantiles = c(0.25, 0.5, 0.75),
  trim = TRUE,
  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
draw_quantiles	draw quantiles for violinplot
trim	whether trim the violin
opt_pancan	specify one dataset for some molercular profiles

Value

a ggplot object

Examples

## Not run: 
p <- vis_pcawg_dist(Gene = "TP53")

## End(Not run)

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