pheatmap实用参数（二）

鞍注塔 · 5 天前

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正文从这里开始

# Show text within cells
pheatmap(test, display_numbers = TRUE)
pheatmap(test, display_numbers = TRUE, number_format = "\\%.1e")
pheatmap(test, display_numbers = TRUE, display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test)))

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# legend（图例）的设置选项
pheatmap(test) # p1
pheatmap(test, legend_breaks = -1:7) # p2
pheatmap(test, legend_breaks = 1:6, legend_labels = c("6","6", "6", "6", "6", "6")) # p3
pheatmap(test, legend_breaks = 9:14, legend_labels = c("6","6", "6", "6", "6", "6")) # p4

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pheatmap函数会在内部算出legend的数值范围，本例中大概是 -1:7
在数值范围内，我们可以设定legend_breaks，以及对legend_breaks这个label的文本展示
legend_breaks和legend_labels是有一个对应关系的，否则报错如下
Error in pheatmap(test, legend_breaks = 1:6, legend_labels =
c(“6”, “6”, : Lengths of legend_breaks and legend_labels must be
the same
假如我们的设定范围超出，就如p4所示

# Fix cell sizes and save to file with correct size
pheatmap(test, cellwidth = 15, cellheight = 12, main = "Example heatmap") # the title of the plot
pheatmap(test, cellwidth = 15, cellheight = 12, fontsize = 8, filename = "test.pdf") # save to pdf
# Change angle of text in the columns (0, 45, 90, 270 and 315)
pheatmap(test, angle_col = "45")
pheatmap(test, angle_col = "0")

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有关annotation

# Generate annotations for rows and columns（先造数据）
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 = "")
# Display row and color annotations
pheatmap(test, annotation_col = annotation_col, cluster_cols = F)
pheatmap(test, annotation_col = annotation_col, annotation_legend = FALSE, cluster_cols = F)
pheatmap(test, annotation_row = annotation_row, cluster_rows = F)

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annotation数据首先要组织成dataframe，dataframe中的rownames要和注释项进行对应，
而column就是要展示的注释条，每个column都会生成一个注释条来显示
annotation_col/row 默认会有legend配合展示，annotation_legend = FALSE可以去掉legend

# Specify colors （自定义注释条颜色）
ann_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)
pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = ann_colors)

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注释条颜色数据要组织成list（list的灵活性就在此处凸显出来了），
list中的每个元素名作为对应项（对应前述dataframe中的colnames），
同时可以进一步为attribute指定颜色，例如
CT1 = "#1B9E77", CT2 = "#D95F02"

参考资料

pheatmap帮助文档

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