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
)

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

Value

a ggplot object or dataframe

Examples

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