R语言绘制热图——pheatmap
pheatmap简介: Pretty Heatmaps——Implementation of heatmaps that offers more control over dimensions and appearance.
- library(pheatmap)
- #创建数据集test测试矩阵
- test = matrix(rnorm(200), 20, 10)
- test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
- test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
- test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
- colnames(test) = paste("Test", 1:10, sep = "")
- rownames(test) = paste("Gene", 1:20, sep = "")
- # 用pheatmap函数画热图
- pheatmap(test)
- <table class="NormalTable "><tbody><tr><td width="534"> </td></tr><tr><td width="534"><span class="fontstyle0">
- </span><span style="font-family: Simsun;font-size:14px;">pheatmap(test, cluster_row = FALSE, legend_breaks = -1:4, legend_labels = c("0",</span></td></tr></tbody></table>
- "1e-4", "1e-3", "1e-2", "1e-1", "1"))#可自己设置图例
pheatmap(test, display_numbers = TRUE, number_format = "%.2f", number_color="purple") #"%.2f"表示保留小数点后两位
- # 在热图格子里展示文本
- pheatmap(test, display_numbers = TRUE)
- pheatmap(test, display_numbers = TRUE, number_format = "\%.1e")
- pheatmap(test, display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test)))#还可以自己设定要显示的内容;
#pheatmap参数设置改变每个格子的大小
pheatmap(test, cellwidth = 15, cellheight = 12, main = "Example heatmap", fontsize = 8, filename = "test.pdf") #main可设置热图的标题,fontsize设置字体大小,filename可直接将热图存出,支持格式png, pdf, tiff, bmp, jpeg,并且可以通过width, height设置图片的大小;
- #pheatmap还可以显示行或列的分组信息,支持多种分组;
- annotation_col = data.frame(CellType = factor(rep(c("CT1", "CT2"), 5)), Time = 1:5)
- rownames(annotation_col) = paste("Test", 1:10, sep = "")
- annotation_row = data.frame(GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6))))
- rownames(annotation_row) = paste("Gene", 1:20, sep = "")
- pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row)
- #设定各个分组的颜色
- ann_colors = list(Time = c("white", "firebrick"), #连续数值型分组可设置成渐变
- CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
- GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E"))
- pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row,
- annotation_colors = ann_colors)
#pheatmap还能够根据特定的条件将热图分隔开;
# cutree_rows, cutree_cols:根据行列的聚类数将热图分隔开;
pheatmap(test,cutree_rows=3,cutree_cols=2)
# cutree_rows, cutree_cols:根据行列的聚类数将热图分隔开;
pheatmap(test,cutree_rows=3,cutree_cols=2)
- #还可以自己设定各个分组的颜色
- ann_colors = list(Time = c("white", "firebrick"), #连续数值型分组可设置成渐变
- CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
- GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E"))
- pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row,
- annotation_colors = ann_colors)
- #还可以利用gaps_row, gaps_col自己设定要分隔开的位置
- pheatmap(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14),
- cutree_col = 2)
转载自:http://blog.csdn.net/sinat_38163598/article/details/72770404