熱圖pheatmap代碼

## ftp://cran.r-project.org/pub/R/web/packages/pheatmap/pheatmap.pdf# Create test matrix## Just replace the test matrix with your own data.test = matrix(rnorm(200), 20, 10)test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4colnames(test) = paste("Test", 1:10, sep = "")rownames(test) = paste("Gene", 1:20, sep = "")# Draw heatmapspheatmap(test)pheatmap(test, kmeans_k = 2)pheatmap(test, scale = "row", clustering_distance_rows = "correlation")pheatmap(test, color = colorRampPalette(c("navy", "white", "firebrick3"))(50) )pheatmap(test, cluster_row = FALSE)pheatmap(test, legend = FALSE)# Show text within cellspheatmap(test, display_numbers = TRUE)pheatmap(test, display_numbers = TRUE, number_format = "\%.1e")pheatmap(test, display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test)))pheatmap(test, cluster_row = FALSE, legend_breaks = -1:4, legend_labels = c("0","1e-4", "1e-3", "1e-2", "1e-1", "1"))# Fix cell sizes and save to file with correct sizepheatmap(test, cellwidth = 15, cellheight = 12, main = "Example heatmap")pheatmap(test, cellwidth = 15, cellheight = 12, fontsize = 8, filename = "test.pdf")# Generate annotations for rows and columnsannotation_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 = "")# Display row and color annotationspheatmap(test, annotation_col = annotation_col)pheatmap(test, annotation_col = annotation_col, annotation_legend = FALSE)pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row)# Specify colorsann_colors = list(Time = c("white", "firebrick"),CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E"))pheatmap(test, annotation_col = annotation_col, annotation_colors = ann_colors, main = "Title")pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row,annotation_colors = ann_colors)pheatmap(test, annotation_col = annotation_col, annotation_colors = ann_colors[2])# Gaps in heatmapspheatmap(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14))pheatmap(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14),cutree_col = 2)# Show custom strings as row/col nameslabels_row = c("", "", "", "", "", "", "", "", "", "", "", "", "", "", "","", "", "Il10", "Il15", "Il1b")pheatmap(test, annotation_col = annotation_col, labels_row = labels_row)# Specifying clustering from distance matrixdrows = dist(test, method = "minkowski")dcols = dist(t(test), method = "minkowski")pheatmap(test, clustering_distance_rows = drows, clustering_distance_cols = dcols)# Modify ordering of the clusters using clustering callback optioncallback = function(hc, mat){sv = svd(t(mat))$v[,1]dend = reorder(as.dendrogram(hc), wts = sv)as.hclust(dend)}pheatmap(test, clustering_callback = callback)## Not run:# Same using dendsort packagelibrary(dendsort)callback = function(hc, ...){dendsort(hc)}pheatmap(test, clustering_callback = callback)## End(Not run)
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