make_lr_target_prior_cor_heatmap Plot Ligand-Receptor–>Target gene links that are both supported by prior knowledge and have correlation in expression
Arguments
- lr_target_prior_cor_filtered
Data frame filtered from `lr_target_prior_cor` (= output of `multi_nichenet_analysis` or `lr_target_prior_cor_inference`). Filter should be done to keep onl LR–>Target links that are both supported by prior knowledge and correlation in terms of expression.
- add_grid
add a ggplot-facet grid to easier link LR pairs to target genes. Default: TRUE.
Examples
if (FALSE) { # \dontrun{
library(dplyr)
lr_network = readRDS(url("https://zenodo.org/record/3260758/files/lr_network.rds"))
lr_network = lr_network %>% dplyr::rename(ligand = from, receptor = to) %>% dplyr::distinct(ligand, receptor)
ligand_target_matrix = readRDS(url("https://zenodo.org/record/3260758/files/ligand_target_matrix.rds"))
sample_id = "tumor"
group_id = "pEMT"
celltype_id = "celltype"
batches = NA
contrasts_oi = c("'High-Low','Low-High'")
contrast_tbl = tibble(contrast = c("High-Low","Low-High"), group = c("High","Low"))
output = multi_nichenet_analysis(
sce = sce,
celltype_id = celltype_id,
sample_id = sample_id,
group_id = group_id,
batches = batches,
lr_network = lr_network,
ligand_target_matrix = ligand_target_matrix,
contrasts_oi = contrasts_oi,
contrast_tbl = contrast_tbl
)
lr_target_prior_cor_filtered = output$lr_target_prior_cor %>% filter(scaled_prior_score > 0.50 & (pearson > 0.66 | spearman > 0.66))
lr_target_prior_cor_heatmap = make_lr_target_prior_cor_heatmap(lr_target_prior_cor_filtered)
} # }