vis_gene_cor_cancer {UCSCXenaShiny}

Visualize Gene-Gene Correlation in a TCGA Cancer Type

Description

Visualize Gene-Gene Correlation in a TCGA Cancer Type

Usage

vis_gene_cor_cancer(
  Gene1 = "CSF1R",
  Gene2 = "JAK3",
  data_type1 = "mRNA",
  data_type2 = "mRNA",
  purity_adj = TRUE,
  cancer_choose = "GBM",
  use_regline = TRUE,
  cor_method = "spearman",
  use_all = FALSE,
  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"

purity_adj

whether performing partial correlation adjusted by purity

cancer_choose

TCGA cohort name, e.g. "ACC".

use_regline

if TRUE, add regression line.

cor_method

correlation method.

use_all

use all sample, default FALSE.

alpha

dot alpha.

color

dot color.

opt_pancan

specify one dataset for some molercular profiles