revisions_update_v2

README.md

@@ -3,8 +3,8 @@
 This repository includes essential scripts for producing final tables and figures embedded in the following manuscript:  
 **Scarfò et al**,_The Fc receptor CD32 identifies human hemogenic endothelial cells irreversibly bound to the endothelial-to-hematopoietic transition_ 
 
-PubMed:  
-DOI:  
+PubMed: 38594587
+DOI: 10.1038/s41556-024-01403-0
 GEO: GSE223223
 
 ---

scRNAseq/ED_Figure5_plots.R

@@ -3,12 +3,15 @@ suppressPackageStartupMessages(library(monocle3))
 suppressPackageStartupMessages(library(ggplot2))
 suppressPackageStartupMessages(library(dplyr))
 suppressPackageStartupMessages(library(ComplexHeatmap))
+suppressPackageStartupMessages(library(viridis))
+suppressPackageStartupMessages(library(outliers))
+suppressPackageStartupMessages(library(R.utils))
 
 
 # ED_Fig5B ----------------------------------------------------------------
 
 ## load scRNAseq data from public dataset GSE162950
-load("Scarfo_HEC2023/scRNAseq/seurat_object.Rdata")
+load("Scarfo_HEC2023/scRNAseq/sample_final.Rdata")
 sample <- SetIdent(sample, value = sample@meta.data$seurat_clusters)
 DimPlot(sample, label=TRUE, group.by = "seurat_clusters")
 sample@meta.data[["orig.ident"]] <- factor(sample@meta.data[["orig.ident"]], 
@@ -24,7 +27,7 @@ DimPlot(sample,
         label=F,
         repel = T,
         reduction="umap", 
-        group.by="orig.ident", 
+        group.by="orig.ident",
         pt.size=0.1,
         cols = c("AGM_CS10_Liu" = "#00BFC4",
                  "AGM_CS11_Liu" = "#00A9FF",
@@ -50,7 +53,7 @@ FeaturePlot(sample,
 
 # ED_Fig5E ----------------------------------------------------------------
 
-install_github("sturgeonlab/Luff-etal-2021/SingleR/versioncontrolscripts")
+devtools::install_github("sturgeonlab/Luff-etal-2021/SingleR/versioncontrolscripts")
 library(versioncontrolscripts)
 
 ## load reference dataset
@@ -58,7 +61,7 @@ cd32_dll4 <- read.table("Scarfo_HEC2023/BulkRNAseq_2/featureCounts_results_tpm.t
                         header=T, sep="\t")
 
 ## load Seurat data
-load("Scarfo_HEC2023/scRNAseq/seurat_object.Rdata")
+load("Scarfo_HEC2023/scRNAseq/sample_final.Rdata")
 sample <- SetIdent(sample, value = sample@meta.data$seurat_clusters)
 sample_noYS <- subset(sample, orig.ident != "YolkSac_CS11_Liu")
 sample_noYS@meta.data[["orig.ident"]] <-

scRNAseq/Fig4_plots.R

@@ -122,7 +122,7 @@ degs_clu11_vs_clu16_17 <- FindMarkers(object = runx1, ident.1 = 11, ident.2 = c(
 
 ## GSEA
 adj.pval.thr <- 0.05
-gmt.obj <- read.gmt("Scarfo_HEC2023/BulkRNAseq_1/c5.all.v7.2.symbols.gmt")
+gmt.obj <- read.gmt("Scarfo_HEC2023/scRNAseq/c5.all.v7.2.symbols.gmt")
 comp <- c("clu11_vs_clu0_1_2", "clu11_vs_clu16_17")
 for (i in comp) {
   degs <- get(paste("degs",i,sep="_"))