Question

我正在尝试用大量数据绘制火山图。在此处显示一些数据。

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数据框tab7 <- structure(list(logFC = c(-1.27422400347856, -0.972370320302353, -1.63545104297305, 0.921263558062452, -0.922767678335555, 1.12992019747864, -1.12813908449641, -0.886389856541233, -1.56395091318283, -0.787704367926754, 0.774615263438003, -1.00983166398568, 1.26941043079936, 0.796918483265524, -0.918242602294084, -0.832196243332996, 1.03096613040452, -0.817670622470357, 0.932412638932054, -1.51103619988004, 0.99279720767736, -0.723506437294531, 0.832067216048265, 0.839856396735337, -0.882234889894418), logCPM = c(7.86936217233427, 6.33767227465018, 5.14411397560036, 6.5874873826811, 7.82025605146652, 5.39870254174873, 5.32742166278357, 6.82202548031827, 3.08154645281093, 11.718268197204, 7.12821560768394, 5.61968280451023, 3.49750759570402, 7.11160629416375, 8.84669666906905, 6.74763398946045, 6.47266715414911, 8.68269736238628, 4.95579660996355, 3.19010537271808, 4.40038075369154, 8.15304798507271, 5.51204801844412, 6.55289240838477, 5.30047595313181 ), F = c(82.3844641280083, 57.1521525156373, 63.0298758207238, 49.4757942110162, 47.8613242874421, 45.4868410091626, 45.1572301486676, 43.7556847965406, 42.3072570929808, 38.9673540472504, 38.7844055524106, 37.9172543011411, 37.1949696821981, 36.4845161241415, 36.388796490688, 36.1521771859631, 37.1195555247141, 35.1179262289968, 34.9714174442816, 34.3515229787112, 33.8072274933505, 33.4471746407308, 32.1242403799937, 31.5096611721688, 31.4822805974465), PValue = c(8.42825601917746e-09, 1.74097802848866e-07, 2.5202773507131e-07, 5.34483590370978e-07, 6.87453204425229e-07, 1.00657587023585e-06, 1.06245353897287e-06, 1.34100176471235e-06, 1.7151684753499e-06, 3.0945677492103e-06, 3.19932402461853e-06, 3.75155343906861e-06, 4.2915391212445e-06, 4.90669309108533e-06, 4.99670077770197e-06, 5.22705003318299e-06, 5.94436067086159e-06, 6.37969536054904e-06, 6.56435248175749e-06, 7.41302885498296e-06, 8.25780079812361e-06, 8.87426754732628e-06, 1.16112919352203e-05, 1.31868786236996e-05, 1.32623209940135e-05 ), FDR = c(0.000124215637210637, 0.00123812825316032, 0.00123812825316032, 0.00196930478872187, 0.0020263370653638, 0.00223692003676889, 0.00223692003676889, 0.00247046050104133, 0.00280868366552298, 0.00428651249771163, 0.00428651249771163, 0.00460753288208276, 0.00481476646181568, 0.00481476646181568, 0.00481476646181568, 0.00481476646181568, 0.00509186457242852, 0.00509186457242852, 0.00509186457242852, 0.00546266096323694, 0.00579540324584504, 0.0059449525051134, 0.00744031393657724, 0.00748287613133365, 0.00748287613133365), Significant = c("FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05", "FDR < 0.05"), genelabels = c("FOSL1", "TEAD4", "STC2", "SNORA28", "SRRM1", "SNORA38", "MGRN1", "HEATR2", "VDR", "SERPINE1", "DPY19L1", "PPRC1", "IFIT1", "ARL6IP5", "SRRM2", "", "", "", "", "", "", "", "", "", "")), row.names = c("FOSL1", "TEAD4", "STC2", "SNORA28", "SRRM1", "SNORA38", "MGRN1", "HEATR2", "VDR", "SERPINE1", "DPY19L1", "PPRC1", "IFIT1", "ARL6IP5", "SRRM2", "ARHGAP17", "SNORA34", "HMOX1", "SNORA46", "HSF2BP", "SNORA66", "BAG3", "SEPP1", "ARL4C", "SLC7A5"), class = "data.frame")具有基因标签，其中包含logFC和FDR详细信息。

使用tab7和数据绘制火山图。我用来绘制火山图的代码在这里。

geom_label_repel

情节看起来像这样

在上面的图中，logFC阳性的基因标签与logFC阴性的标签重叠。我希望基因标签的左侧logFC为负，右侧为logFC。

感谢您的帮助。谢谢。

Answer 1

我们可以分别添加带有不同 xlim 范围的负值和正值标签。

注意：我删除了所有不相关的美学内容，以将重点放在问题上：

如何在标签的左侧保留负值，在右侧保留正值

library(ggplot2)
library(ggrepel)

ggplot(tab7, aes(logFC, -log10(FDR))) +
  geom_point()  +
  geom_label_repel(data = tab7[ tab7$FDR < 0.05 & tab7$logFC < 0, ], 
                   aes(label = genelabels),
                   xlim = c(NA, -1), # <--- here
                   seed = 1) +
  geom_label_repel(data = tab7[ tab7$FDR < 0.05 & tab7$logFC > 0, ], 
                   aes(label = genelabels),
                   xlim = c(1, NA),  # <--- here
                   seed = 1) +
  scale_x_continuous(limits = c(-4, 4))

还有一些用于火山图的专用R包，例如，请参见：

EnhancedVolcano

如何使用geom_label_repel避免图中的标签重叠？

1 个答案: