UCSCXenaShiny (version 2.2.0)

vis_gene_cross_omics: Visualize cross-omics of one gene among pan-cancers

Description

Visualize cross-omics of one gene among pan-cancers

Usage

vis_gene_cross_omics(
  gene = "TP53",
  tumor_projects = NULL,
  tumor_samples = NULL,
  n_trans = 5,
  n_methy = 5,
  seed = 42,
  add_mean_trans = TRUE,
  add_mean_methy = TRUE,
  pval_mrna = c(0.05, 0.01, 0.001),
  return_list = FALSE
)

Value

funkyheatmap

Arguments

gene

a gene symbol identifier (e.g., "TP53")

tumor_projects

Select specific TCGA projects. Default NULL, indicating all TCGA projects.

tumor_samples

Select specific tumor samples. Default NULL, indicating all tumor samples.

n_trans

The number of sampling transcripts or specific transcript identifiers.

n_methy

The number of sampling CpG sites or specific CpG identifiers.

seed

The seed of sampling.

add_mean_trans

Add overall column to display the mean values of all gene's transcripts.

add_mean_methy

Add overall column to display the mean values of all gene's cpg sites.

pval_mrna

The P value thresholds

return_list

TRUE returns a list including plot object and data. FALSE just returns plot.