Adding Fig2C dataset markers

Figures_2CDEF.R

@@ -18,7 +18,7 @@ library(dplyr)
 
 # load seurat object
 
-obj <- readRDS("CultureDataset.rds")
+obj <- readRDS("Fig2C_Dataset.rds")
 
 # setting color palette:
 

Figures_2G.R

@@ -18,7 +18,7 @@ library(dplyr)
 
 # load seurat object
 
-obj <- readRDS("CultureDataset.rds")
+obj <- readRDS("Fig2C_Dataset.rds")
 obj <- subset(obj, cells = WhichCells(object = obj,expression = orig.ident %in% c("C04","C02","C03")))
 obj <- SetIdent(object = obj, value = "Population")
 

FindAllMarkers_Population_dataset_Fig2C.R

+library(Seurat)
+library(ggplot2)
+library(harmony)
+library(RColorBrewer)
+library(plotly)
+library(htmlwidgets)
+library(ComplexHeatmap)
+library(openxlsx)
+library(dplyr)
+library(future)
+library(gridExtra)
+
+options(future.globals.maxSize = 96 * 1024^3)
+
+cur_dir <- getwd()
+obj <- readRDS(file = "Fig2C_Dataset.rds")
+markers_dir <- "tables/"
+
+sampleid <- "Full"
+integration.var <- "orig.ident"
+
+# setup multiprocess with future library
+
+no_cores <- availableCores() - 1
+plan("multicore", workers = no_cores)
+
+markers <- list()
+start <- Sys.time()
+obj <- SetIdent(object = obj, value = "Population")
+markers <- FindAllMarkers(object = obj, logfc.threshold = 0, min.pct = 0.2, only.pos = F, return.thresh = 1.1)
+end <- Sys.time()
+time2process <- as.numeric(end - start, units = "secs")
+print(paste0("Time to complete Markers on", length(Cells(obj)), " cells with ", no_cores, " Population ", time2process))
+saveRDS(markers, file = paste0(markers_dir,sampleid,"_GSEA_markers_Population_Fig2C_Dataset.rds"))
+
+df <- split(x = markers, f = markers$cluster)
+write.xlsx(x = df, file = paste0(markers_dir,sampleid,"_GSEA_markers_Population_Fig2C_Dataset.xlsx"), asTable = T, overwrite = T)
+
+