compute_LR_interact: Compute and plot the LR interactions for one factor

In scITD: Single-Cell Interpretable Tensor Decomposition

Compute and plot the LR interactions for one factor

Description

Compute and plot the LR interactions for one factor

Usage

compute_LR_interact(
  container,
  lr_pairs,
  sig_thresh = 0.05,
  percentile_exp_rec = 0.75,
  add_ld_fact_sig = 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
lr_pairs	data.frame Data of ligand-receptor pairs. First column should be ligands and second column should be one or more receptors separated by an underscore such as receptor1_receptor2 in the case that multiple receptors are required for signaling.
sig_thresh	numeric The p-value significance threshold to use for module- factor associations and ligand-factor associations (default=0.05)
percentile_exp_rec	numeric The percentile above which the top donors expressing the ligand all must be expressing the receptor (default=0.75)
add_ld_fact_sig	logical Set to TRUE to append a heatmap showing significance of associations between each ligand hit and each factor (default=TRUE)
ncores	numeric The number of cores to use (default=container$experiment_params$ncores)

Value

The LR analysis results heatmap as ComplexHeatmap object. Adjusted p-values for all results are placed in container$lr_res.

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