如何修复在 R 中切断 y 轴文本的图像保存？

Question

我有一个热图，其中 y 轴的文本不断被截断。无论我尝试在 RStudio 导出中手动保存图像，还是使用：

，文本都会被截断

png(filename)
Heatmap(pathways, name = "log p-value", column_title = "Genesets", 
        cluster_rows = FALSE,  row_names_side = "left", col = col_fun)
dev.off()

我如何更改图形宽度和高度也无关紧要 - 更改这些参数会更改热图方块的大小，但截断的文本始终是相同的数量。

示例图片：

我已经裁掉了 X 轴，因为我无法共享它，如图所示，我只有 Y 轴有问题。另外作为参考，我使用 complexheatmap 包制作了热图。

编辑：尝试此操作似乎也无济于事：

par(mar=c(100,100,100,100)+10)
png(filename='test.png', width=700, height=700)
Heatmap(df_pathways, name = "log p-value", column_title = "Genesets", 
        cluster_rows = FALSE, cluster_columns = FALSE,  row_names_side = "left", col = col_fun)
graphics.off()

示例输入数据：

pathways <-
structure(list(Group1 = c(9.420318259, 4.836092781, 5.561049165, 
8.190548144, 6.71227316, 4.095942487, 4.992794151, 5.552164863, 
4.34153332, 5.895592291, 7.553546365, 4.992782053, 6.053009309, 
6.860701322, 5.801092847, 5.148352899, 4.890727291, 4.228175167, 
5.804415571, 4.589825753), Group2 = c(14.57805564, 10.81418654, 
11.09736375, 10.32521712, 12.0145571, 10.07735354, 10.02001419, 
9.218294382, 10.09808164, 8.177240205, 8.657878442, 9.835699421, 
8.687931231, 8.31684452, 8.798453748, 7.760651767, 7.982599836, 
8.300396581, 8.249833908, 7.951599435), Group3 = c(14.49131554, 
13.3205827, 12.12174012, 10.44766272, 11.01869555, 11.09934699, 
11.24184793, 10.09879495, 9.876597118, 9.654484641, 10.91601179, 
9.873567424, 8.476802302, 8.318460384, 7.975284646, 7.409538041, 
8.258878348, 6.821340952, 7.075861702, 7.922657108), Group4 = c(11.44447147, 
10.69676399, 9.595976655, 8.394853352, 8.82546953, 7.762112046, 
7.146613208, 7.773426526, 7.445916643, 6.928897709, 6.969416034, 
7.90504739, 5.971561206, 6.126050462, 6.208332721, 6.93495916, 
6.529806574, 5.727539932, 7.097356964, 4.882623805), Group5 = c(22.86835197, 
12.70083108, 10.05632122, 8.487520597, 4.207896212, 10.08721586, 
9.726807084, 9.539543451, 12.26094928, 12.23048716, 7.885614665, 
6.993219914, 11.35470645, 11.22311857, 10.94297858, 9.214002287, 
7.197041788, 10.59080554, 5.08232173, 9.237584441), Group6 = c(10.62687539, 
12.39464562, 8.714396722, 7.436886904, 9.303280092, 8.266037496, 
8.650863908, 7.753285867, 6.151852334, 7.227066955, 5.589700078, 
7.271066145, 7.172215654, 6.000920914, 6.458410247, 5.790443124, 
7.461916094, 7.272885252, 5.318945244, 6.308454021), Group7 = c(11.09404106, 
11.13903127, 9.363613884, 8.811864251, 9.255305005, 8.082707248, 
7.101057322, 8.064874227, 7.29823506, 7.154725479, 7.256169907, 
7.56145848, 6.155332798, 6.349384361, 6.420303272, 7.232379137, 
6.821000583, 5.934088344, 7.368454621, 5.0727153)), row.names = c("Cardiac Hypertrophy Signaling (Enhanced)", 
"Estrogen Receptor Signaling", "Role of NFAT in Cardiac Hypertrophy", 
"Protein Kinase A Signaling", "Molecular Mechanisms of Cancer", 
"Opioid Signaling Pathway", "Hepatic Fibrosis Signaling Pathway", 
"Gap Junction Signaling", "G-Protein Coupled Receptor Signaling", 
"White Adipose Tissue Browning Pathway", "Sperm Motility", "Factors Promoting Cardiogenesis in Vertebrates", 
"Nitric Oxide Signaling in the Cardiovascular System", "Relaxin Signaling", 
"Cellular Effects of Sildenafil (Viagra)", "Insulin Secretion Signaling Pathway", 
"Colorectal Cancer Metastasis Signaling", "Ovarian Cancer Signaling", 
"PPARÎ±/RXRÎ± Activation", "Corticotropin Releasing Hormone Signaling"
), class = "data.frame")

Answer 1

请参阅我上面的评论：当您说“y 轴的文本”时，我认为您是在谈论截断的行标签。如果这确实是您正在努力解决的问题，那么将 Heatmap 参数 row_names_max_width 从默认值 unit(6, "cm") 增加到类似 row_names_max_width = unit(12, "cm") 的值应该可以让您容纳更长的行标签。

library(ComplexHeatmap)

## using your provided data as df_pathways

Heatmap(df_pathways, name = "log p-value", column_title = "Genesets", 
        row_names_max_width = unit(12, "cm"),
        cluster_rows = FALSE, cluster_columns = FALSE,  row_names_side = "left")
#> Warning: The input is a data frame, convert it to the matrix.

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