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
)

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

Value

a ggplot object or a tibble data.frame

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")
}