ComplexHeatmap是一个很好用的绘制热图的R包。这篇文章主要介绍Complexheatmap::pheatmap绘图字体设置。
在原函数中没有设置字体的参数。查看有关font的参数比较表如下：
表头为Arguments in pheatmap::pheatmap()和Identical settings/arguments in ComplexHeatmap::Heatmap()
参考：https://jokergoo.github.io/2020/05/06/translate-from-pheatmap-to-complexheatmap/
其实我们通过上述比较表可以看出
Complexheatmap::pheatmap中一些参数是调用Complexheatmap::Heatmap中的一些参数来调整绘图参数的。首先，我想到了测试了下直接传入Heatmap的参数到pheatmap，但是其中一些参数如果重新设置会显示冲突。
Error in (function (matrix, col, name, na_col = "grey", color_space = "LAB", :
正式参数"column_names_gp"有多个与之相对应的实际参数
排除了这种方式之外，我测试时发现另一种可行的方法！首先将绘图函数保存到一个变量中，测试代码如下：
library("ComplexHeatmap")
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 = "")
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 = "")
# Specify colors
ann_colors = list(
Time = c("white", "firebrick"),
CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E")
)
p <- pheatmap(test,
annotation_col = annotation_col,
annotation_row = annotation_row,
annotation_colors = ann_colors,
color = colorRampPalette(c("#0000FF", "#FFFCC8", "#FF0000"))(100),
border_color = NA,
cellwidth =NA, cellheight = NA,
cluster_rows = TRUE,
cluster_cols = TRUE,
legend = TRUE,
main = "jsd diversity distance",
fontsize = 10,
fontsize_row = 8,
fontsize_col = 10,
display_numbers = FALSE, number_format = "%.1f", number_color="Black", fontsize_number=4,
# display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test))
angle_col = "90", # options (0, 45, 90, 270 and 315)
# show_rownames = TRUE, show_colnames = TRUE
annotation_legend = TRUE
)
查看p可以看出是一个S4对象，我们可以找下其中可以设置字体的参数，可以根据参数的名称来找
行标题字体设置示例
这里我指定参数的代码如下
p@row_title_param$gp$fontfamily = "serif" # 行标题
其他的参数也是类似的。
font_family = "serif"
p@column_names_param$gp$fontfamily = font_family # 列名称
p@row_names_param$gp$fontfamily = font_family # 行名称
p@row_title_param$gp$fontfamily = font_family # 行标题p@column_title_param$gp$fontfamily = font_family # 列标题（图标题）
除了，legend设置的参数在设置完成后可能会有报错，需要指定gpar来设置：
p@matrix_legend_param = gpar(title_gp = gpar(fontfamily = font_family), labels_gp = gpar(fontfamily = font_family))
最后是行分类，和列分类的字体（包括对应的图例字体）
p@top_annotation@anno_list[[coltype]]@name_param$gp$fontfamily = font_family # 列分类标题
p@top_annotation@anno_list[[coltype]]@legend_param = gpar(title_gp = gpar(fontfamily = font_family), labels_gp = gpar(fontfamily = font_family))
p@left_annotation@anno_list[[rowtype]]@name_param$gp$fontfamily = font_family # 行分类标题
p@left_annotation@anno_list[[rowtype]]@legend_param = gpar(title_gp = gpar(fontfamily = font_family), labels_gp = gpar(fontfamily = font_family))
最后来show一下对比图吧
修改前：默认字体
修改后：Times字体
参考链接：
- https://jokergoo.github.io/ComplexHeatmap-reference/book/
- pheatmap无缝迁移到ComplexHeatmap https://www.plob.org/article/24019.html
