UCSCXenaShiny (version 2.1.0)

vis_gene_TIL_cor: Heatmap for Correlation between Gene and Tumor Immune Infiltration (TIL)

Description

Heatmap for Correlation between Gene and Tumor Immune Infiltration (TIL)

Usage

vis_gene_TIL_cor(
  Gene = "TP53",
  cor_method = "spearman",
  data_type = "mRNA",
  sig = c("B cell_TIMER", "T cell CD4+_TIMER", "T cell CD8+_TIMER", "Neutrophil_TIMER",
    "Macrophage_TIMER", "Myeloid dendritic cell_TIMER"),
  Plot = "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").

cor_method

correlation method

data_type

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

sig

Immune Signature, default: result from TIMER

Plot

output the plot directly, default 'TRUE'

opt_pancan

specify one dataset for some molercular profiles

Examples

if (FALSE) {
p <- vis_gene_TIL_cor(Gene = "TP53")
}