make_lr_target_prior_cor_heatmap: make_lr_target_prior_cor_heatmap

In saeyslab/multinichenetr: MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

make_lr_target_prior_cor_heatmap

Description

make_lr_target_prior_cor_heatmap Plot Ligand-Receptor–>Target gene links that are both supported by prior knowledge and have correlation in expression

Usage

make_lr_target_prior_cor_heatmap(lr_target_prior_cor_filtered, add_grid = TRUE)

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.

Value

ggplot object with plot of LR–>Target links

Examples

## Not run: 
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) 

## End(Not run)

saeyslab/multinichenetr documentation built on Jan. 15, 2025, 7:55 p.m.