vis_pcawg_gene_cor: Visualize Gene-Gene Correlation in TCGA
In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

vis_pcawg_gene_cor

R Documentation

Visualize Gene-Gene Correlation in TCGA

Description

Visualize Gene-Gene Correlation in TCGA

Usage

vis_pcawg_gene_cor(
  Gene1 = "CSF1R",
  Gene2 = "JAK3",
  data_type1 = "mRNA",
  data_type2 = "mRNA",
  cor_method = "spearman",
  purity_adj = TRUE,
  use_log_x = FALSE,
  use_log_y = FALSE,
  use_regline = TRUE,
  dcc_project_code_choose = "BLCA-US",
  use_all = FALSE,
  filter_tumor = TRUE,
  alpha = 0.5,
  color = "#000000",
  opt_pancan = .opt_pancan
)

Arguments

`Gene1`	a molecular identifier (e.g., "TP53") or a formula specifying genomic signature (`"TP53 + 2 * KRAS - 1.3 * PTEN"`).
`Gene2`	a molecular identifier (e.g., "TP53") or a formula specifying genomic signature (`"TP53 + 2 * KRAS - 1.3 * PTEN"`).
`data_type1`	choose gene profile type for the first gene, including "mRNA","transcript","methylation","miRNA","protein","cnv_gistic2"
`data_type2`	choose gene profile type for the second gene, including "mRNA","transcript","methylation","miRNA","protein","cnv_gistic2"
`cor_method`	correlation method
`purity_adj`	whether performing partial correlation adjusted by purity
`use_log_x`	if `TRUE`, log X values.
`use_log_y`	if `TRUE`, log Y values.
`use_regline`	if `TRUE`, add regression line.
`dcc_project_code_choose`	select project code.
`use_all`	use all sample, default `FALSE`.
`filter_tumor`	whether use tumor sample only, default `TRUE`
`alpha`	dot alpha.
`color`	dot color.
`opt_pancan`	specify one dataset for some molercular profiles