get_all_lds_factor_plots {scITD}

Generate loadings heatmaps for all factors

Description

Generate loadings heatmaps for all factors

Usage

get_all_lds_factor_plots(
  container,
  use_sig_only = FALSE,
  nonsig_to_zero = FALSE,
  annot = "none",
  pathways_list = NULL,
  sim_de_donor_group = NULL,
  sig_thresh = 0.05,
  display_genes = FALSE,
  gene_callouts = FALSE,
  callout_n_gene_per_ctype = 5,
  callout_ctypes = NULL,
  show_var_explained = TRUE,
  reset_other_factor_plots = TRUE
)

Arguments

container

environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses

use_sig_only

logical If TRUE, includes only significant genes from jackstraw in the heatmap. If FALSE, includes all the variable genes. (default = FALSE)

nonsig_to_zero

logical If TRUE, makes the loadings of all nonsignificant genes 0 (default=FALSE)

annot

character If set to "pathways" then creates an adjacent heatmap showing which genes are in which pathways. If set to "sig_genes" then creates an adjacent heatmap showing which genes were significant from jackstraw. If set to "none" no adjacent heatmap is plotted. (default="none")

pathways_list

list A list of sets of pathways for each factor. List index should be the number corresponding to the factor. (default=NULL)

sim_de_donor_group

numeric To plot the ground truth significant genes from a simulation next to the heatmap, put the number of the donor group that corresponds to the factor being plotted. Here it should be a vector corresponding to the factors. (default=NULL)

sig_thresh

numeric Pvalue significance threshold to use. If use_sig_only is TRUE the threshold is used as a cutoff for genes to include. If annot is "sig_genes" this value is used in the gene significance colormap as a minimum threshold. (default=0.05)

display_genes

logical If TRUE, displays the names of gene names (default=FALSE)

gene_callouts

logical If TRUE, then adds gene callout annotations to the heatmap (default=FALSE)

callout_n_gene_per_ctype

numeric To use if gene_callouts is TRUE. Sets the number of largest magnitude significant genes from each cell type to include in gene callouts. (default=5)

callout_ctypes

list To use if gene_callouts is TRUE. Specifies which cell types to get gene callouts for. Each entry of the list should be a character vector of ctypes for the respective factor. If NULL, then gets gene callouts for largest magnitude significant genes for all cell types. (default=NULL)

show_var_explained

logical If TRUE then shows an anottation with the explained variance for each cell type (default=TRUE)

reset_other_factor_plots

logical If TRUE then removes any existing loadings plots (default=TRUE)

Value

The project container with the list of all loadings heatmap plots placed in container$plots$all_lds_plots.

Examples

test_container <- get_all_lds_factor_plots(test_container)