vis_toil_TvsN: Visualize Pan-cancer TPM (tumor (TCGA) vs Normal (TCGA &...

Description Usage Arguments Value Examples

View source: R/vis_pancan_value.R

Description

Visualize Pan-cancer TPM (tumor (TCGA) vs Normal (TCGA & GTEx))

Usage

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vis_toil_TvsN(
  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"),
  TCGA.only = FALSE,
  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

TCGA.only

include samples only from TCGA dataset

draw_quantiles

draw quantiles for violinplot

trim

whether trim the violin

Value

a ggplot object

Examples

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## Not run: 
p <- vis_toil_TvsN(Gene = "TP53", Mode = "Violinplot", Show.P.value = FALSE, Show.P.label = FALSE)
p <- vis_toil_TvsN(Gene = "TP53", Mode = "Boxplot", Show.P.value = FALSE, Show.P.label = FALSE)

## End(Not run)

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