Commit c0939a58 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

updated crosstalk file

parent f11162e7
......@@ -60,8 +60,7 @@ if(!file.exists("./lung_rmd_res/Lung_cell_specific_markers.txt")) {
message("File './lung_rmd_res/Lung_cell_specific_markers.txt' does not exist, run 'SC_analysis_airways.Rmd' to generate it.")
} else {
mnv_airway_cells <- read.table(file = "./lung_rmd_res/Lung_cell_specific_markers.txt",
sep = "\t", header = T) %>%
filter(abs(avg_log2FC) > 0.3 & p_val_adj < 0.1)
sep = "\t", header = T) %>% filter(p_val_adj < 0.1)
### We select three "secretory" subtypes to create overlays
ariw_sec1_cells <- create_minerva_overlay(filter(mnv_airway_cells, cluster == "Secretory1"),
......@@ -77,8 +76,7 @@ if(!file.exists("./gut_rmd_res/degs_bys_vs_mock_24h_illeum.txt")) {
} else {
### We select one bystander cell type from the gut organoids
mnv_bys_mock_24h_il <- read.table("./gut_rmd_res/degs_bys_vs_mock_24h_illeum.txt",
header = T, sep = "\t") %>%
filter(abs(avg_log2FC) > 0.3 & p_val_adj < 0.1)
header = T, sep = "\t") %>% filter(p_val_adj < 0.1)
sel_bys <- "Illeum_24h_Inmature Enterocyte 2_Bystander_v_Illeum_Mock_Inmature Enterocyte 2_Non-Infected"
bys_mock_24h_il_imm_ent <- create_minerva_overlay(filter(mnv_bys_mock_24h_il, comparison == sel_bys),
name_hgnc_map = name_hgncs,
......@@ -91,8 +89,7 @@ if(!file.exists("./gut_rmd_res/degs_inf_vs_mock_illeum_24h.txt")) {
} else {
### We select one infected cell type from the gut organoids
mnv_inf_mock_24h_il <- read.table("./gut_rmd_res/degs_inf_vs_mock_illeum_24h.txt",
header = T, sep = "\t") %>%
filter(abs(avg_log2FC) > 0.3 & p_val_adj < 0.1)
header = T, sep = "\t") %>% filter(p_val_adj < 0.1)
sel_inf <- "Illeum_24h_Inmature Enterocyte 2_Infected_v_Illeum_Mock_Inmature Enterocyte 2_Non-Infected"
inf_mock_24h_il_imm_ent <- create_minerva_overlay(filter(mnv_inf_mock_24h_il, comparison == sel_inf),
name_hgnc_map = name_hgncs,
......
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