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