run_gsea_one_factor: Run gsea separately for all cell types of one specified...

In scITD: Single-Cell Interpretable Tensor Decomposition

Run gsea separately for all cell types of one specified factor and plot results

Description

Run gsea separately for all cell types of one specified factor and plot results

Usage

run_gsea_one_factor(
  container,
  factor_select,
  method = "fgsea",
  thresh = 0.05,
  db_use = "GO",
  signed = TRUE,
  min_gs_size = 15,
  max_gs_size = 500,
  reset_other_factor_plots = FALSE,
  draw_plot = TRUE,
  ncores = container$experiment_params$ncores
)

Arguments

container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
factor_select	numeric The factor of interest
method	character The method of gsea to use. Can either be "fgsea", "fgsea_special or "hypergeometric". (default="fgsea")
thresh	numeric Pvalue significance threshold to use. Will include gene sets in resulting heatmap if pvalue is below this threshold for at least one cell type. (default=0.05)
db_use	character The database of gene sets to use. Database options include "GO", "Reactome", "KEGG", and "BioCarta". More than one database can be used. (default="GO")
signed	logical If TRUE, uses signed gsea. If FALSE, uses unsigned gsea. Currently only works with fgsea method (default=TRUE)
min_gs_size	numeric Minimum gene set size (default=15)
max_gs_size	numeric Maximum gene set size (default=500)
reset_other_factor_plots	logical Set to TRUE to set all other gsea plots to NULL (default=FALSE)
draw_plot	logical Set to TRUE to show the plot. Plot is stored regardless. (default=TRUE)
ncores	numeric The number of cores to use (default=container$experiment_params$ncores)

Value

A stacked heatmap plot of the gsea results in the slot container$plots$gsea$<Factor#>. The heatmaps show adjusted p-values for the enrichment of each gene set in each cell type for the selected factor. The top heatmap shows enriched gene sets among the positive loading genes and the bottom heatmap shows enriched gene sets among the negative loading genes for the factor.

Examples

test_container <- run_gsea_one_factor(test_container, factor_select=1,
method="fgsea", thresh=0.05, db_use="Hallmark", signed=TRUE)

scITD documentation built on Sept. 8, 2023, 5:11 p.m.