getwd() library(pheatmap) library(RColorBrewer) #setwd("/Users/kshitij/Desktop/Melbourne work/UNIMEL_DP/Analysis/CAT_BAT_analysis/Plutea_MAGs/New_Analysis/Metabolism/Enrichm_metabolic_selective_modules/") setwd("/Users/kshitij/Desktop/Melbourne work/UNIMEL_DP/Analysis/CAT_BAT_analysis/Ipalifera_MAGs/Metabolism/enrichm_metabolic_KEGG_module75/") data =read.table(file.choose(),sep="\t",header=T,row.names = 1) head(data) cols = colorRampPalette(c("white", "black"))(50) data_tax=data.frame("Taxonomy"=c(rep("Alphaproteobacteria",37),rep("Bacteroidia", 5),rep("Binatia",1),rep("Chlorobia", 10),rep("Clostridia", 3),rep("Cyanobacteriia", 1),rep("Desulfarculia", 1),rep("Desulfobacteria", 4),rep("Gammaproteobacteria", 26),rep("Gemmatimonadetes", 2),rep("Phycisphaerae", 11),rep("Planctomycetes", 2),rep("SAR324", 4),rep("UBA11346", 1),rep("UBA1135", 1),rep("UBA4882", 1),rep("UBA9160", 3),rep("Vampirovibrionia", 1),rep("Verrucomicrobiae",3))) rownames(data_tax)=rownames(data) #newCols <- colorRampPalette(grDevices::stepped(length(unique(data_tax$Taxonomy)))) newCols<-colorRampPalette(hcl.colors(19,palette = "Purple-Orange")) mycolors <- newCols(length(unique(data_tax$Taxonomy))) names(mycolors) <- unique(data_tax$Taxonomy) mycolors <- list(Taxonomy = mycolors) pheatmap(t(data[,1:9]),cluster_rows = F,cluster_cols = F,cellwidth = 5,cellheight = 5,border_color = "white",fontsize = 4,gaps_col=c(37,42,43,53,56,57,58,62,88,90,101,103,107,108,109,110,113,114),gaps_row = c(5,8),color = cols,annotation_col=data_tax,annotation_colors = mycolors) ##### Ipalifera metabolism plot###############33 setwd("/Users/kshitij/Desktop/Melbourne work/UNIMEL_DP/Analysis/CAT_BAT_analysis/Ipalifera_MAGs/Metabolism/enrichm_metabolic_KEGG_module75/") data =read.table(file.choose(),sep="\t",header=T,row.names = 1) head(data) cols = colorRampPalette(c("white", "black"))(50) data_tax=data.frame("Taxonomy"=c(rep("Alphaproteobacteria",30),rep("Bacteroidia", 3),rep("Calditrichia",1),rep("Cyanobacteriia", 3),rep("Gammaproteobacteria", 10),rep("Gemmatimonadetes", 2),rep("Phycisphaerae", 6),rep("Planctomycetes", 8),rep("Sumerlaeia", 1),rep("UBA9160", 1),rep("Verrucomicrobiae",3),rep("WYAZ01",1))) rownames(data_tax)=rownames(data) #newCols <- colorRampPalette(grDevices::stepped(length(unique(data_tax$Taxonomy)))) newCols<-colorRampPalette(hcl.colors(19,palette = "Purple-Orange")) mycolors <- newCols(length(unique(data_tax$Taxonomy))) names(mycolors) <- unique(data_tax$Taxonomy) mycolors <- list(Taxonomy = mycolors) pheatmap(t(data[,1:9]),cluster_rows = F,cluster_cols = F,cellwidth = 5,cellheight = 5,border_color = "white",fontsize = 4,gaps_col=c(30,33,34,37,47,49,55,63,64,65,68,69),gaps_row = c(5,8),color = cols,annotation_col=data_tax,annotation_colors = mycolors)