UCSCXenaShiny (version 2.1.0)

vis_gene_pw_cor: Visualize Correlation between Gene and Pathway signature Score

Description

Visualize Correlation between Gene and Pathway signature Score

Usage

vis_gene_pw_cor(
  Gene = "TP53",
  data_type = "mRNA",
  pw_name = "HALLMARK_ADIPOGENESIS",
  cancer_choose = "GBM",
  use_regline = TRUE,
  cor_method = "spearman",
  use_all = FALSE,
  alpha = 0.5,
  color = "#000000",
  filter_tumor = TRUE,
  opt_pancan = .opt_pancan
)

Value

a ggplot object or dataframe

Arguments

Gene

a molecular identifier (e.g., "TP53") or a formula specifying genomic signature ("TP53 + 2 * KRAS - 1.3 * PTEN").

data_type

choose gene profile type, including "mRNA", "transcript", "protein", "mutation", "cnv", "methylation", "miRNA".

pw_name

the queried Pathway name, see the supported pathway from 'load("toil_sig_score")'default is NULL

cancer_choose

select cancer cohort(s)

use_regline

if TRUE, add regression line.

cor_method

select correlation coefficient (pearson/spearman)

use_all

use all sample, default FALSE.

alpha

dot alpha.

color

dot color.

filter_tumor

whether use tumor sample only, default TRUE

opt_pancan

specify one dataset for some molercular profiles

Examples

if (FALSE) {
vis_gene_pw_cor(Gene = "TP53", data_type = "mRNA", 
                pw_name = "HALLMARK_ADIPOGENESIS",
                cancer_choose = "BRCA")
}