vis_ccle_gene_cor {UCSCXenaShiny}

Visualize CCLE Gene Expression Correlation

Description

Visualize CCLE Gene Expression Correlation

Usage

vis_ccle_gene_cor(
  Gene1 = "CSF1R",
  Gene2 = "JAK3",
  data_type1 = "mRNA",
  data_type2 = "mRNA",
  cor_method = "spearman",
  use_log_x = FALSE,
  use_log_y = FALSE,
  use_regline = TRUE,
  SitePrimary = "prostate",
  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"

cor_method

correlation method

use_log_x

if TRUE, log X values.

use_log_y

if TRUE, log Y values.

use_regline

if TRUE, add regression line.

SitePrimary

select cell line origin tissue.

use_all

use all sample, default FALSE.

alpha

dot alpha.

color

dot color.

opt_pancan

specify one dataset for some molercular profiles

Value

a ggplot object