vis_pcawg_dist: Visualize molecular profile in PCAWG

Description Usage Arguments Value Examples

View source: R/vis_pcawg_value.R

Description

Visualize molecular profile in PCAWG

Usage

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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
)

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" (-2, -1, 0, 1, 2), "cnv_gistic2", "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

Value

a ggplot object

Examples

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

## End(Not run)

UCSCXenaShiny documentation built on Nov. 29, 2021, 9:06 a.m.