Workflow(3) Basic Visualization

Posted on 2023-02-21 Edited on 2023-02-22 In Workflow

Workflow(3) Basic Visualization

准备工作

1.R studio

2.代码

2.1 volcano plot code

if(!require(ggplot2)) install.packages("ggplot2")   
if(!require(ggrepel)) install.packages("ggrepel")
if(!require(dplyr))install.packages("dplyr")
#这些步骤表示查询这些包有没有安装，如果没有则安装，第一次使用时需要注意，再次使用时不用再粘贴了
library(ggplot2)
library(ggrepel)
library(dplyr)

绘制可以标注蛋白名的火山图

    setwd("E://Datasetlocalize/People/HSY/CRC/20210729_CRC_Glycosylation_project/Glycosylation/Volcano/")
    data=read.table(file="GlyBvsAvolcano.txt",header=T,sep="\t")
    library(ggpubr)
    pdf(file = "GlyBAvolcano.pdf",width = 20,height = 15)
    ggscatter(data, 
          x = "fold.change", 
          y ="t.test.p.value",
          ylab ="-log10(Pvalue)",
          xlab = "log2(FoldChange)",
          size=3,
          color = "Difference",
          label = "ProteinName",font.label = c(24,"bold","navy"),  #darkblue00008B
          repel = TRUE,
          palette = c("#FC4E07","#00AFBB","#999999"),  #FC4E07red,#00AFBBblue，#999999gray
          label.select = c("LAMP1","ITB3","CD36","KNG1","ITA6","CD34","APMAP","A2MG","ICAM1","CD68")
    +
      xlim(-11.5,11.5)+
      geom_hline(yintercept=-log10(0.05),linetype=4)+
      geom_vline(xintercept=c(-1,1),linetype=4)+
      #theme_bw()+
      theme(legend.title = element_blank())+
      font("xlab",size = 30)+font("ylab",size = 30)+
      font("subtitle",size=30)+font("caption",size = 20)+
      font("xy.text",size = 18)+
      font("legend.text",size = 20)
    dev.off()

```    

#### 2.2 heatmap    
内容比较多，后续会增加注释
```R
setwd("F:/Taogroup/ZH/20201205_pca_exosome_auto_12_PEAKS_10/1213third/")
library(pheatmap)
data=read.table(file="proZ.txt",header=T,sep="\t")
rownames(data)=data[,9]
pheatmap(data[,1:8],show_rownames =T,cluster_cols = F,fontsize_row=7)
#pheatmap(data[,2:3],cluster_cols = FALSE,main = "heatmap",show_rownames =TRUE,cellwidth=40,cellheight = 20,fontsize=18,treeheight_row = 20)
bk <- c(seq(-2,-0.1,by=0.1),seq(0,2,by=0.1))

pheatmap(data[,1:12],show_rownames =F,cluster_cols = F,cluster_rows=F,fontsize_row=3,colorRampPalette(colors = c("blue","white","red"))(100))

pheatmap(data[,2:3],cluster_cols = FALSE,show_rownames = FALSE,border_color=NA, fontsize_row=6,main = "ProteinDiff",fontsize=10,color = c(colorRampPalette(colors = c("blue","white"))(length(bk)/2),colorRampPalette(colors = c("white","red"))(length(bk)/2)),
         legend_breaks=seq(0,10,0.5),breaks=bk,
         clustering_method="complete",
         treeheight_row=50
)

setwd("F://Taogroup/People/HSY/MM/Gly/MMGlyPeaks/MMGlyPeaks530_PEAKS_14/3group/")
library(pheatmap)
data=read.table(file="3groupforheatmap.txt",header=T,sep="\t")
rownames(data)=data[,13]
pheatmap(data[,1:12],show_rownames =F,cluster_cols = F,cluster_rows = F,fontsize_row=7)
pheatmap(data[,1:12],show_rownames =F,cluster_cols = F,fontsize_row=7,
         clustering_distance_rows = "euclidean", clustering_method = "complete",
          cutree_rows = 5) 


pheatmap(data[,1:12], treeheight_col = 0, treeheight_row = 20, border_color = "grey", 
         cellwidth = 10, cellheight = 0.1, fontsize = 4, show_rownames = FALSE, 
         cluster_col = FALSE, height = 1, clustering_distance_rows = "euclidean", 
         clustering_method = "complete", cutree_rows = 5)


#color = c(colorRampPalette(colors = c("blue","white"))(length(bk)/2),colorRampPalette(colors = c("white","red"))(length(bk)/2)),
#legend_breaks=seq(-9,9,2),breaks=bk
#single,ward.D,complete

#scale data by row
scale_rows <- function (x) {
  m = apply(x, 1, mean, na.rm = T)
  s = apply(x, 1, sd, na.rm = T)
  return((x - m)/s)
}
mat = switch('row', none = data[,2:10], row = scale_rows(data[,2:10]), column = t(scale_rows(t(data[2:10]))))

#cluster row
d = dist(mat, method = 'euclidean')
tree = hclust(d, method = 'complete')

#cut tree
v = cutree(tree, 5)[tree$order]
gaps = which((v[-1] - v[-length(v)]) != 0)

#get cluster gene data
gene.cluster <- as.data.frame(v)
gene.cluster$gene <- strsplit(rownames(gene.cluster),'[.]')[,1]
write.table(gene.cluster, "gene.cluster.txt", row.names = FALSE, quote = FALSE, sep = "\t")


setwd("F:/Taogroup/People/HSY/CRC/20210519/Full/result/")
library(pheatmap)
data=read.table(file="3groupforheatmap.txt",header=T,sep="\t")
rownames(data)=data[,11]
annotation_row = data.frame(
  Cluster = factor(rep(c("Cluster1", "Cluster2", "Cluster3","Cluster4","Cluster5"), c(429, 353, 113,593,645)))
)
#add annotation， the number in the second parentheses represent the quant of regard cluster
rownames(annotation_row) = rownames(data)
pheatmap(data[,1:9],show_rownames =F,cluster_cols = F,cluster_rows=F,fontsize_row=7,annotation_row=annotation_row)


library(ComplexHeatmap)
library(circlize)
data=data.matrix(data)
color = colorRamp2(seq(0, 100,length=2), c("gray95","firebrick3"))
labels_row=c("GYPA","CDH5","SELP")
ht = Heatmap(data,name = "Positive beads(%)",col = color,rect_gp = gpar(col = "white", lwd = 2),
             cluster_columns = FALSE, cluster_rows = FALSE, 
             width = ncol(data)*unit(5, "mm"), height = nrow(data)*unit(6, "mm"),
             show_row_names = F, show_column_names = F,
             heatmap_legend_param = list(legend_direction="horizontal",
                                              legend_width=unit(5,"cm"),title_position="lefttop")
             )
draw(ht,heatmap_legend_side="bottom")


setwd("E://Datasetlocalize/People/HSY/CRC/20210729_CRC_Glycosylation_project/Glycosylation/")
library(pheatmap)
data=read.table(file="tangjihuaheatmap.txt",header=T,sep="\t")
data=data.matrix(data)
pheatmap(data[,1:9],show_rownames =F,fontsize_row=3,cluster_col=F,cluster_rows = F,
         cellwidth = 24,
         colorRampPalette(colors = c("forestgreen","white","red"))(100),
         gaps_row = c(242,458,504,666,690,695,918))

)

#xiugai zhushidaozuobian
library(grid)
library(gtable)

# Modified pheatmap:::heatmap_motor
heatmap_motor <- function (matrix, border_color, cellwidth, cellheight, tree_col, 
                           tree_row, treeheight_col, treeheight_row, filename, width, 
                           height, breaks, color, legend, annotation_row, annotation_col, 
                           annotation_colors, annotation_legend, annotation_names_row, 
                           annotation_names_col, main, fontsize, fontsize_row, fontsize_col, 
                           hjust_col, vjust_col, angle_col, fmat, fontsize_number, number_color, 
                           gaps_col, gaps_row, labels_row, labels_col, ...) 
{
  lo = pheatmap:::lo(coln = labels_col, rown = labels_row, nrow = nrow(matrix), 
                     ncol = ncol(matrix), cellwidth = cellwidth, cellheight = cellheight, 
                     treeheight_col = treeheight_col, treeheight_row = treeheight_row, 
                     legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, 
                     annotation_colors = annotation_colors, annotation_legend = annotation_legend, 
                     annotation_names_row = annotation_names_row, annotation_names_col = annotation_names_col, 
                     main = main, fontsize = fontsize, fontsize_row = fontsize_row, 
                     fontsize_col = fontsize_col, angle_col = angle_col, gaps_row = gaps_row, 
                     gaps_col = gaps_col, ...)
  res = lo$gt
  mindim = lo$mindim
  if (!is.na(filename)) {
    if (is.na(height)) {
      height = convertHeight(gtable_height(res), "inches", valueOnly = T)
    }
    if (is.na(width)) {
      width = convertWidth(gtable_width(res), "inches", valueOnly = T)
    }
    r = regexpr("\\.[a-zA-Z]*$", filename)
    if (r == -1) 
      stop("Improper filename")
    ending = substr(filename, r + 1, r + attr(r, "match.length"))
    f = switch(ending, pdf = function(x, ...) pdf(x, ...), 
               png = function(x, ...) png(x, units = "in", res = 300, 
                                          ...), jpeg = function(x, ...) jpeg(x, units = "in", 
                                                                             res = 300, ...), jpg = function(x, ...) jpeg(x, 
                                                                                                                          units = "in", res = 300, ...), tiff = function(x, 
                                                                                                                                                                         ...) tiff(x, units = "in", res = 300, compression = "lzw", 
                                                                                                                                                                                   ...), bmp = function(x, ...) bmp(x, units = "in", 
                                                                                                                                                                                                                    res = 300, ...), stop("File type should be: pdf, png, bmp, jpg, tiff"))
    f(filename, height = height, width = width)
    gt = heatmap_motor(matrix, cellwidth = cellwidth, cellheight = cellheight, 
                       border_color = border_color, tree_col = tree_col, 
                       tree_row = tree_row, treeheight_col = treeheight_col, 
                       treeheight_row = treeheight_row, breaks = breaks, 
                       color = color, legend = legend, annotation_col = annotation_col, 
                       annotation_row = annotation_row, annotation_colors = annotation_colors, 
                       annotation_legend = annotation_legend, annotation_names_row = annotation_names_row, 
                       annotation_names_col = annotation_names_col, filename = NA, 
                       main = main, fontsize = fontsize, fontsize_row = fontsize_row, 
                       fontsize_col = fontsize_col, hjust_col = hjust_col, 
                       vjust_col = vjust_col, angle_col = angle_col, fmat = fmat, 
                       fontsize_number = fontsize_number, number_color = number_color, 
                       labels_row = labels_row, labels_col = labels_col, 
                       gaps_col = gaps_col, gaps_row = gaps_row, ...)
    grid.draw(gt)
    dev.off()
    return(gt)
  }
  if (mindim < 3) 
    border_color = NA
  if (!is.na(main)) {
    elem = pheatmap:::draw_main(main, fontsize = 1.3 * fontsize, ...)
    res = gtable_add_grob(res, elem, t = 1, l = 3, name = "main", 
                          clip = "off")
  }
  if (!pheatmap:::is.na2(tree_col) & treeheight_col != 0) {
    elem = pheatmap:::draw_dendrogram(tree_col, gaps_col, horizontal = T)
    res = gtable_add_grob(res, elem, t = 2, l = 3, name = "col_tree")
  }
  if (!pheatmap:::is.na2(tree_row) & treeheight_row != 0) {
    elem = pheatmap:::draw_dendrogram(tree_row, gaps_row, horizontal = F)
    res = gtable_add_grob(res, elem, t = 4, l = 1, name = "row_tree")
  }
  elem = pheatmap:::draw_matrix(matrix, border_color, gaps_row, gaps_col, 
                                fmat, fontsize_number, number_color)
  res = gtable_add_grob(res, elem, t = 4, l = 3, clip = "off", 
                        name = "matrix")
  if (length(labels_col) != 0) {
    pars = list(labels_col, gaps = gaps_col, fontsize = fontsize_col, 
                hjust_col = hjust_col, vjust_col = vjust_col, angle_col = angle_col, 
                ...)
    elem = do.call(pheatmap:::draw_colnames, pars)
    res = gtable_add_grob(res, elem, t = 5, l = 3, clip = "off", 
                          name = "col_names")
  }
  if (length(labels_row) != 0) {
    pars = list(labels_row, gaps = gaps_row, fontsize = fontsize_row, 
                ...)
    elem = do.call(pheatmap:::draw_rownames, pars)
    res = gtable_add_grob(res, elem, t = 4, l = 3, clip = "off", 
                          name = "row_names")
  }
  if (!pheatmap:::is.na2(annotation_col)) {
    converted_annotation = convert_annotations(annotation_col, 
                                               annotation_colors)
    elem = pheatmap:::draw_annotations(converted_annotation, border_color, 
                                       gaps_col, fontsize, horizontal = T)
    res = gtable_add_grob(res, elem, t = 3, l = 3, clip = "off", 
                          name = "col_annotation")
    if (annotation_names_col) {
      elem = pheatmap:::draw_annotation_names(annotation_col, fontsize, 
                                              horizontal = T)
      res = gtable_add_grob(res, elem, t = 3, l = 4, clip = "off", 
                            name = "col_annotation_names")
    }
  }
  if (!pheatmap:::is.na2(annotation_row)) {
    converted_annotation = convert_annotations(annotation_row, 
                                               annotation_colors)
    elem = pheatmap:::draw_annotations(converted_annotation, border_color, 
                                       gaps_row, fontsize, horizontal = F)
    res = gtable_add_grob(res, elem, t = 4, l = 2, clip = "off", 
                          name = "row_annotation")
    if (annotation_names_row) {
      elem = pheatmap:::draw_annotation_names(annotation_row, fontsize, 
                                              horizontal = F, hjust_col = hjust_col, vjust_col = vjust_col, 
                                              angle_col = angle_col)
      res = gtable_add_grob(res, elem, t = 5, l = 2, clip = "off", 
                            name = "row_annotation_names")
    }
  }
  annotation = c(annotation_col[length(annotation_col):1], 
                 annotation_row[length(annotation_row):1])
  annotation = annotation[unlist(lapply(annotation, function(x) !pheatmap:::is.na2(x)))]
  if (length(annotation) > 0 & annotation_legend) {
    elem = pheatmap:::draw_annotation_legend(annotation, annotation_colors, 
                                             border_color, fontsize = fontsize, ...)
    t = ifelse(is.null(labels_row), 4, 3)
    res = gtable_add_grob(res, elem, t = t, l = 6, b = 5, 
                          clip = "off", name = "annotation_legend")
  }
  if (!pheatmap:::is.na2(legend)) {
    elem = pheatmap:::draw_legend(color, breaks, legend, fontsize = fontsize, 
                                  ...)
    t = ifelse(is.null(labels_row), 4, 3)
    res = gtable_add_grob(res, elem, t = t, l = 5, b = 5, 
                          clip = "off", name = "legend")
  }
  return(res)
}

# Modified pheatmap:::lo    
lo <- function (rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, 
                treeheight_col, treeheight_row, legend, annotation_row, annotation_col, 
                annotation_colors, annotation_legend, annotation_names_row, 
                annotation_names_col, main, fontsize, fontsize_row, fontsize_col, 
                angle_col, gaps_row, gaps_col, ...) 
{
  if (!is.null(coln[1]) | (!pheatmap:::is.na2(annotation_row) & annotation_names_row)) {
    if (!is.null(coln[1])) {
      t = coln
    }
    else {
      t = ""
    }
    tw = strwidth(t, units = "in", cex = fontsize_col/fontsize)
    if (annotation_names_row) {
      t = c(t, colnames(annotation_row))
      tw = c(tw, strwidth(colnames(annotation_row), units = "in"))
    }
    longest_coln = which.max(tw)
    gp = list(fontsize = ifelse(longest_coln <= length(coln), 
                                fontsize_col, fontsize), ...)
    coln_height = unit(1, "grobheight", textGrob(t[longest_coln], 
                                                 rot = angle_col, gp = do.call(gpar, gp))) + unit(10, 
                                                                                                  "bigpts")
  }
  else {
    coln_height = unit(5, "bigpts")
  }
  if (!is.null(rown[1])) {
    t = rown
    tw = strwidth(t, units = "in", cex = fontsize_row/fontsize)
    if (annotation_names_col) {
      t = c(t, colnames(annotation_col))
      tw = c(tw, strwidth(colnames(annotation_col), units = "in"))
    }
    longest_rown = which.max(tw)
    gp = list(fontsize = ifelse(longest_rown <= length(rown), 
                                fontsize_row, fontsize), ...)
    rown_width = unit(1, "grobwidth", textGrob(t[longest_rown], 
                                               rot = 0, gp = do.call(gpar, gp))) + unit(10, "bigpts")
  }
  else {
    rown_width = unit(5, "bigpts")
  }
  gp = list(fontsize = fontsize, ...)
  if (!pheatmap:::is.na2(legend)) {
    longest_break = which.max(nchar(names(legend)))
    longest_break = unit(1.1, "grobwidth", 
                         textGrob(as.character(names(legend))[longest_break], 
                                  gp = do.call(gpar, gp)))
    title_length = unit(1.1, "grobwidth", textGrob("Scale", 
                                                   gp = gpar(fontface = "bold", ...)))
    legend_width = unit(12, "bigpts") + longest_break * 1.2
    legend_width = max(title_length, legend_width)
  }
  else {
    legend_width = unit(0, "bigpts")
  }
  if (is.na(main)) {
    main_height = unit(0, "npc")
  }
  else {
    main_height = unit(1.5, "grobheight", textGrob(main, 
                                                   gp = gpar(fontsize = 1.3 * fontsize, ...)))
  }
  textheight = unit(fontsize, "bigpts")
  if (!pheatmap:::is.na2(annotation_col)) {
    annot_col_height = ncol(annotation_col) * (textheight + 
                                                 unit(2, "bigpts")) + unit(2, "bigpts")
    t = c(as.vector(as.matrix(annotation_col)), colnames(annotation_col))
    annot_col_legend_width = unit(1.2, "grobwidth", textGrob(t[which.max(nchar(t))], 
                                                             gp = gpar(...))) + unit(12, "bigpts")
    if (!annotation_legend) {
      annot_col_legend_width = unit(0, "npc")
    }
  }
  else {
    annot_col_height = unit(0, "bigpts")
    annot_col_legend_width = unit(0, "bigpts")
  }
  if (!pheatmap:::is.na2(annotation_row)) {
    annot_row_width = ncol(annotation_row) * (textheight + 
                                                unit(2, "bigpts")) + unit(2, "bigpts")
    t = c(as.vector(as.matrix(annotation_row)), colnames(annotation_row))
    annot_row_legend_width = unit(1.2, "grobwidth", textGrob(t[which.max(nchar(t))], 
                                                             gp = gpar(...))) + unit(12, "bigpts")
    if (!annotation_legend) {
      annot_row_legend_width = unit(0, "npc")
    }
  }
  else {
    annot_row_width = unit(0, "bigpts")
    annot_row_legend_width = unit(0, "bigpts")
  }
  annot_legend_width = max(annot_row_legend_width, annot_col_legend_width)
  treeheight_col = unit(treeheight_col, "bigpts") + unit(5, 
                                                         "bigpts")
  treeheight_row = unit(treeheight_row, "bigpts") + unit(5, 
                                                         "bigpts")
  if (is.na(cellwidth)) {
    mat_width = unit(1, "npc") - rown_width - legend_width - 
      treeheight_row - annot_row_width - annot_legend_width
  }
  else {
    mat_width = unit(cellwidth * ncol, "bigpts") + length(gaps_col) * 
      unit(4, "bigpts")
  }
  if (is.na(cellheight)) {
    mat_height = unit(1, "npc") - main_height - coln_height - 
      treeheight_col - annot_col_height
  }
  else {
    mat_height = unit(cellheight * nrow, "bigpts") + length(gaps_row) * 
      unit(4, "bigpts")
  }
  gt = gtable(widths = unit.c(treeheight_row, rown_width,  
                              mat_width, treeheight_row, legend_width, annot_legend_width), 
              heights = unit.c(main_height, treeheight_col, annot_col_height, 
                               mat_height, coln_height), vp = viewport(gp = do.call(gpar, 
                                                                                    gp)))
  cw = convertWidth(mat_width - (length(gaps_col) * unit(4, 
                                                         "bigpts")), "bigpts", valueOnly = T)/ncol
  ch = convertHeight(mat_height - (length(gaps_row) * unit(4, 
                                                           "bigpts")), "bigpts", valueOnly = T)/nrow
  mindim = min(cw, ch)
  res = list(gt = gt, mindim = mindim)
  return(res)
}

# Modified pheatmap:::draw_rownames      
draw_rownames <- function (rown, gaps, ...) 
{
  coord = pheatmap:::find_coordinates(length(rown), gaps)
  y = unit(1, "npc") - (coord$coord - 0.5 * coord$size)
  res = textGrob(rown, x = unit(-3, "bigpts"), y = y, vjust = 0.5, 
                 hjust = 1, gp = gpar(...))
  return(res)
}

assignInNamespace(x="draw_rownames", value=draw_rownames, ns="pheatmap")
assignInNamespace(x="lo", value=lo, ns="pheatmap")
assignInNamespace(x="heatmap_motor", value=heatmap_motor, ns="pheatmap") 


#fenkai hua
library(ComplexHeatmap)
library(circlize)
NDMM = read.table(file = "NDMM.txt",header = T,sep = "\t",row.names = 1)
RRMM = read.table(file = "RRMM.txt",header = T,sep = "\t",row.names = 1)

pdf("positive beads.pdf")#,units = "px")
NDMM = data.matrix(NDMM)
RRMM = data.matrix(RRMM)
color = colorRamp2(seq(0, 100,length=2), c("gray95","maroon"))
labels_row=c("BCMA","CD47","CD147","CD98","CD38")
labels_col=c("Isotype","Control","NDMM1","NDMM2","NDMM3","NDMM4","Isotype","Control","RRMM1","RRMM2","RRMM3")
ht1=Heatmap(NDMM,name = "Positive beads(%)",col = color,rect_gp = gpar(col = "white", lwd = 2),
            cluster_columns = FALSE, cluster_rows = FALSE, 
            width = ncol(data)*unit(6, "mm"), height = nrow(data)*unit(6, "mm"),
            show_row_names = T, show_column_names = T,row_names_side = "left",column_names_side = "top",column_names_rot = 45,
            heatmap_legend_param = list(legend_direction="horizontal",
                                        legend_width=unit(5,"cm"),title_position="lefttop")
            )
ht2=Heatmap(RRMM,name = "Positive beads(%)",col = color,rect_gp = gpar(col = "white", lwd = 2),
            cluster_columns = FALSE, cluster_rows = FALSE, 
            width = ncol(data)*unit(5, "mm"), height = nrow(data)*unit(6, "mm"),
            show_row_names = T, show_column_names = T,row_names_side = "left",column_names_side = "top",column_names_rot = 45,
            heatmap_legend_param = list(legend_direction="horizontal",
                                        legend_width=unit(5,"cm"),title_position="lefttop")
            )
ht_list = ht1 + ht2
draw(ht_list,heatmap_legend_side="bottom",ht_gap =unit(3,"mm"))
dev.off()




setwd("F:/Taogroup/People/SJ/20220301PRM/heatmap/")
library(pheatmap)
data=read.table(file="salivaheatmap1.txt",header=T,sep="\t",row.names = 1)
annotation_col = read.table(file = "annotation.txt",header=T,sep="\t")
rownames(annotation_col)=colnames(data)
#temp <- as.data.frame(as.numeric(data[2:11,]))
pdf(file = "salivaheatmap.pdf",width = 10,height = 15)
pheatmap(data,show_rownames =F,cluster_cols = F,cluster_rows=F,
         fontsize_row=7,show_colnames = F,
         annotation_col = annotation_col,
         cellwidth = 10,cellheight = 20,
         colorRampPalette(colors = c("#7AC5CD","white","#EE6A50"))(50),
         gaps_col = c(2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32))
dev.off()
         


#将表达数据按照热图的顺序输出
library(pheatmap)
 
exp = read.table("exp_top30.original.txt",header=T,row.names=1,sep="t")
 
result <- pheatmap(data,cluster_cols = F,clustering_distance_rows = "euclidean",clustering_method = "average")
col_oder=result$order # 保存热图列顺序（序号）

row_oder=result$tree_row$order # 保存热图行顺序（序号）

cn_new <- colnames(data)[col_oder] # 保存热图的列名

rn_new <- rownames(data)[row_oder] # 保存热图的行名

new_exp <- matrix(rep(0,ncol(data)*nrow(data)),nrow = nrow(data),ncol = ncol(data))

out <- matrix(rep(0,ncol(data)*nrow(data)),nrow = nrow(data),ncol = ncol(data))

## 将表达量数据读入数据框new_exp,行顺序已经按照热图的顺序重排

for (i in 1:ncol(data)){
  
  new_exp[,i]=data[,i][row_oder]
  
}

rownames(new_exp)=rn_new

colnames(new_exp)=cn_new

write.table(new_exp,"hp_exp.txt",sep="\t") #输出重排后的表达量表

以上代码包括各种功能实现，自定义