plot_heatmap_for_fGSEA_all_clusters: Plot heatmap for GSEA for all comparisons

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Plot heatmap for GSEA for all comparisons

Description

Plot heatmap for GSEA for all comparisons

Usage

plot_heatmap_for_fGSEA_all_clusters(
  fGSEA_results.data.frame,
  isApplyCutoff = F,
  adjusted_pval = 0.25,
  add_small_value = 1e-04,
  use_pvalues_for_clustering = T,
  show_NES_score = T,
  show_only_NES_positive_score = F,
  show_only_NES_negative_score = F,
  custom_order_samples = c(),
  fontsize_row = 5,
  format.digits = 2,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  clustering_method = "complete",
  clustering_distance_rows = "euclidean",
  clustering_distance_cols = "euclidean",
  gaps_row = NULL,
  gaps_col = NULL,
  show_text_for_ns = T
)

Arguments

fGSEA_results.data.frame	The input dataframe for fGSEA analysis results.
isApplyCutoff	is logical. If TRUE, the cutoff will be applied.
adjusted_pval	The cutoff adjusted p-value. Default 0.25
use_pvalues_for_clustering	is logical. If TRUE, the p-values will be used for clustering analysis.
show_NES_score	is logical. If TRUE, the enrichment score will be displayed.
show_only_NES_positive_score	is logical. If TRUE, the only NES positive scores will be displayed.
show_only_NES_negative_score	is logical. If TRUE, the only NES negative scores will be displayed.
custom_order_samples	The vector of input custom order of GSEA comparison on the heatmap.
fontsize_row	The row font size. Default 5
format.digits	The format of digit number shows on the heatmap. Default 2
cluster_rows	is logical. If TRUE, the clustering analysis will be performed by row.
cluster_cols	is logical. If TRUE, the clustering analysis will be performed by column.
clustering_method	The HCL clustering method. Default complete
clustering_distance_rows	The distance of rows for the clustering. Default euclidean
clustering_distance_cols	The distance of columns for the clustering. Default euclidean.
gaps_row	The vector of gaps for row.
gaps_col	The vector of gaps for column.
show_text_for_ns	is logical. If TRUE. The ns or 'non-significant' will be displayed.
object	The SingCellaR object.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.