mat2 = mat rownames(mat2)[1] = paste(c(letters, LETTERS), collapse = "") Heatmap(mat2, name = "mat", row_title = "default row_names_max_width")
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Heatmap(mat2, name = "mat", row_title = "row_names_max_width as length of a*", row_names_max_width = max_text_width( rownames(mat2), gp = gpar(fontsize = 12) ))
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自定义行名/列名，可用于解决原始矩阵行名/列名不能有重复的问题，或使用特殊符号等：
# use a named vector to make sure the correspondance between row names and row labels is correct row_labels = structure(paste0(letters[1:24], 1:24), names = paste0("row", 1:24)) column_labels = structure(paste0(LETTERS[1:24], 1:24), names = paste0("column", 1:24)) row_labels
# clustering is similar as previous heatmap with branches in some nodes in the dendrogram flipped Heatmap(mat, name = "mat", row_split = factor(rep(LETTERS[1:3], 6), levels = LETTERS[3:1]), column_split = factor(rep(letters[1:6], 4), levels = letters[6:1]))
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# now the order is exactly what we set Heatmap(mat, name = "mat", row_split = factor(rep(LETTERS[1:3], 6), levels = LETTERS[3:1]), column_split = factor(rep(letters[1:6], 4), levels = letters[6:1]), cluster_row_slices = FALSE, cluster_column_slices = FALSE)
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2.7.5 分割标题
split = data.frame(rep(c("A", "B"), 9), rep(c("C", "D"), each = 9)) Heatmap(mat, name = "mat", row_split = split, row_title = "%s|%s")
Heatmap(mat, name = "mat", row_split = split, row_title = "there are four slices")
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ht = Heatmap(mat, name = "mat", row_split = split, row_title = "%s|%s") # This row_title is actually a heatmap-list-level row title draw(ht, row_title = "I am a row title")
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Heatmap(mat, name = "mat", row_split = split, row_title = NULL)
r = min(unit.c(w, h))*0.45 if(is.na(go_mat[i, j])) { } elseif(go_mat[i, j] == "W") { grid.circle(x, y, r, gp = gpar(fill = "white", col = "white")) } elseif(go_mat[i, j] == "B") { grid.circle(x, y, r, gp = gpar(fill = "black", col = "black")) } }, col = c("B" = "black", "W" = "white"), show_row_names = FALSE, show_column_names = FALSE, column_title = "One famous GO game", heatmap_legend_param = list(title = "Player", at = c("B", "W"), labels = c("player1", "player2"), border = "black") )
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2.9.2 layer_fun
用法差不多，但是更复杂
# code only for demonstration Heatmap(..., layer_fun = function(j, i, x, y, w, h, fill) {...}) # or you can capitalize the arguments to mark they are vectors, # the names of the argumetn do not matter Heatmap(..., layer_fun = function(J, I, X, Y, W, H, F) {...})
col_fun = colorRamp2(c(-2, 0, 2), c("green", "white", "red")) Heatmap(small_mat, name = "mat", col = col_fun, layer_fun = function(j, i, x, y, width, height, fill) { # since grid.text can also be vectorized grid.text(sprintf("%.1f", pindex(small_mat, i, j)), x, y, gp = gpar(fontsize = 10)) })
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Heatmap(small_mat, name = "mat", col = col_fun, row_km = 2, column_km = 2, layer_fun = function(j, i, x, y, width, height, fill) { v = pindex(small_mat, i, j) grid.text(sprintf("%.1f", v), x, y, gp = gpar(fontsize = 10)) if(sum(v > 0)/length(v) > 0.75) { grid.rect(gp = gpar(lwd = 2, fill = "transparent")) } })
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Heatmap(small_mat, name = "mat", col = col_fun, row_km = 2, column_km = 2, layer_fun = function(j, i, x, y, w, h, fill) { # restore_matrix() is explained after this chunk of code ind_mat = restore_matrix(j, i, x, y) for(ir in seq_len(nrow(ind_mat))) { # start from the second column for(ic in seq_len(ncol(ind_mat))[-1]) { ind1 = ind_mat[ir, ic-1] # previous column ind2 = ind_mat[ir, ic] # current column v1 = small_mat[i[ind1], j[ind1]] v2 = small_mat[i[ind2], j[ind2]] if(v1 * v2 > 0) { # if they have the same sign col = ifelse(v1 > 0, "darkred", "darkgreen") grid.segments(x[ind1], y[ind1], x[ind2], y[ind2], gp = gpar(col = col, lwd = 2)) grid.points(x[c(ind1, ind2)], y[c(ind1, ind2)], pch = 16, gp = gpar(col = col), size = unit(4, "mm")) } } } } )
