Adding Arial family and missing lines

DotPlotVolcano.R

-
 # code for reproducing figures in paper
 # AIM: create a dotplot / heatmap with genes of interest present in the attachment
 # facets by category of interest shown in the excel
@@ -11,6 +10,7 @@ library(DESeq2)
 library(reshape2)
 library(RColorBrewer)
 library(scales)
+library(dplyr)
 
 # loading genelist file and create a dataframe ####
 mydata <- read.xlsx(xlsxFile = "GeneList_Fig2A.xlsx")
@@ -25,7 +25,7 @@ mydata$Cluster[37:45] <- "HSC"
 # remove double entry AKT3
 mydata <- subset(mydata, Gene != "AKT3.1")
 mydata$Cluster <- gsub(pattern = "HSC", replacement = "HSC related", x = mydata$Cluster)
-saveRDS(object = mydata, file = "Gene_list.rds")
+#saveRDS(object = mydata, file = "Gene_list.rds")
 
 # read data analysis input ####
 
@@ -42,6 +42,18 @@ normacounts_NE <- normcounts[,rownames(colannotations)]
 
 goi_expr <- as.matrix(normacounts_NE[mydata$Gene,])
 
+DEGs_d4 <- myexpress$deseq$dge_res$`3DNEd4-2DNEd4`
+DEGs_d4 <- subset.data.frame(DEGs_d4, subset = FDR < 0.05)
+DEGs_d4$Gene <- rownames(DEGs_d4)
+DEGs_d4$isDEGd4 <- "isDEG"
+DEGs_d4 <- subset.data.frame(DEGs_d4, select = c("Gene","isDEGd4"))
+DEGs_d7 <- myexpress$deseq$dge_res$`3DNEd7-2DNEd7`
+DEGs_d7 <- subset.data.frame(DEGs_d7, subset = FDR < 0.05)
+DEGs_d7$Gene <- rownames(DEGs_d7)
+DEGs_d7$isDEGd7 <- "isDEG"
+DEGs_d7 <- subset.data.frame(DEGs_d7, select = c("Gene","isDEGd7"))
+
+
 ## Version with means ####
 
 goi_expr_means_melt <- melt(goi_expr)
@@ -99,7 +111,8 @@ ggplot(goi_expr_melt_2_degannot, mapping = aes(x = variable, y = Gene, fill = va
         panel.background = element_rect(fill = "white"),
         strip.background = element_blank(), 
         panel.spacing = unit(1.3, "lines"), 
-        strip.clip = "off",
+        #strip.clip = "off",
+        text = element_text(family = "Arial"),
         panel.grid = element_line(colour = "lightgrey"), axis.title = element_blank())
 dev.off()
 
@@ -154,6 +167,7 @@ for(tpdata in names(exprlist)){
     theme(legend.position = "bottom", #c(0.2,0.9), 
           legend.key.height = unit(units = "cm", x = 0.2),
           legend.key.width = unit(units = "cm", x = 0.2),
+          text = element_text(family = "Arial"),
           plot.title = element_text(hjust = 0.5)) + 
     ggtitle(paste0("3D vs 2D ", tpdata))
   
@@ -162,3 +176,4 @@ for(tpdata in names(exprlist)){
          width = 6, height = 6, dpi = 300)
 }
 
+