Update plot_Hap_pheatmap.r

plot_Hap_pheatmap.r

@@ -1,26 +1,21 @@
 # 不同组之间有缝隙，更加直观
 library(pheatmap)
-group = read.table("sample_plot.list.txt", stringsAsFactors = F) ##两列，1：ID，2：品种
-names(group) <- c("ID","Group")
-rownames(group) <- group$ID
-group$ID <- NULL
+group = read.table("sample_plot.list.txt", row.names=1, stringsAsFactors = F) # 两列，1：ID，2：品种,ID与txt文件顺序一致
+names(group) <- c("Group")
 
-new_order <- c("JPBC", "Mongolian", "Kazakh", "Yanbian") # 新的组顺序
-group$Group <- factor(group$Group, levels = new_order)
+data=read.table("LRP2BP.SNP.biallele.txt",header=TRUE, stringsAsFactors = F) # 转置后的文件
+data=data.matrix(data)
 
-data2=read.table ("LRP2BP.SNP.biallele.txt", header = TRUE, stringsAsFactors = F) # 转置后的文件
-data2=data.matrix(data2)
-
-annotation_row = data.frame(Group=as.vector(group$Group))
-rownames(annotation_row) = rownames(data2)
-
-names(rowcol) <- unique(annotation_row)
-ra_col <- list(Group=c(JPBC="#873186", Mongolian="#E20593",  Kazakh="#6BB93F", Yanbian="#18A2CA"))
+an_row = data.frame(Group=as.vector(group$Group))
+rownames(an_row)=rownames(data)
+ra_col <- list(Group=c(JPBC="#873186",Mongolian="#E20593",
+                       Kazakh="#6BB93F",Yanbian="#18A2CA"))
 # "#3364BC", "#000000", "#F37020", "#DBB71D"
 gap_line <- c(11,21,32) # 数量划分，分开每组的热图
 
-pheatmap(data2,annotation_row = annotation_row, annotation_colors = ra_col,
-        cluster_row = FALSE,cluster_col = FALSE,
-        gaps_row=gap_line,legend =FALSE,
-        labels_col = rep("",ncol(data2)),labels_row=rep("",nrow(data2)),
-        color=c("#F7F8D5", "#BF3826"), angle_col = "0")
+pheatmap(data,cluster_row=F,cluster_col=F,legend=F,
+         show_rownames=FALSE,show_colnames=FALSE,
+         annotation_legend=T,annotation_names_row=T,
+         annotation_row=an_row,annotation_colors=ra_col,
+         gaps_row=gap_line,
+         color=c("#F7F8D5", "#BF3826"))