vis_pcawg_gene_cor: Visualize Gene-Gene Correlation in TCGA

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

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"
)

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.

Value

a ggplot object

UCSCXenaShiny documentation built on March 7, 2023, 7 p.m.