对ggplots的情节做这样的修改

Question

我有这样的数据

> dput(x)
structure(list(gene = c("14q", "20q", "18q", "4q", "21p", "21q", 
"5q", "22q", "17p", "3p", "9p", "4p", "9q", "19q", "10q", "15q", 
"16p", "19p", "1p", "18p", "16q", "8p"), CNV = c("Deletion", 
"Amplification", "Deletion", "Deletion", "Deletion", "Deletion", 
"Deletion", "Deletion", "Deletion", "Deletion", "Deletion", "Deletion", 
"Deletion", "Deletion", "Deletion", "Deletion", "Deletion", "Deletion", 
"Deletion", "Deletion", "Deletion", "Deletion"), log10_pvalue = c(1.197226275, 
1.88941029, 5.974694135, 5.73754891, 4.995678626, 4.970616222, 
4.793174124, 4.793174124, 4.109020403, 3.524328812, 3.524328812, 
2.823908741, 2.567030709, 2.186419011, 1.769551079, 1.59345982, 
1.59345982, 1.59345982, 1.416801226, 1.195860568, 1.094743951, 
1.087777943), Percentage_altered = c(3000, 5000, 6100, 5300, 
6100, 5600, 4400, 5000, 5000, 4400, 5000, 4700, 3900, 2800, 3300, 
3100, 3300, 3100, 2200, 3600, 3300, 3300), group = c("Responders", 
"Responders", "Non-responders", "Non-responders", "Non-responders", 
"Non-responders", "Non-responders", "Non-responders", "Non-responders", 
"Non-responders", "Non-responders", "Non-responders", "Non-responders", 
"Non-responders", "Non-responders", "Non-responders", "Non-responders", 
"Non-responders", "Non-responders", "Non-responders", "Non-responders", 
"Non-responders")), row.names = c(NA, -22L), class = "data.frame")

我用过这个代码

> p=x %>% 
Warning messages:
1: ggrepel: 6 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
2: ggrepel: 6 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
+     mutate(net_frequency=ifelse(CNV == "Deletion", -Percentage_altered/100, Percentage_altered/100),
+            log10_pvalue = if_else(CNV == "Deletion", log10_pvalue, log10_pvalue)) %>% 
+     ggplot(aes(x = log10_pvalue, y = net_frequency, color = log10_pvalue)) +
+     geom_point(aes(size=Percentage_altered)) +
+     geom_text_repel(aes(label=gene), force=15) +
+     geom_hline(yintercept=0, lty=2) +
+     scale_color_distiller(type = "div",palette = 5) +
+     theme_classic() +
+     facet_wrap(~group)
> p+xlab("-log10(qvalue)")+ylab("Net frequency of gain and deletion (%)")+theme(
+     plot.title = element_text(color="black", size=14, face="bold.italic"),
+     axis.title.x = element_text(color="black", size=14, face="bold"),
+     axis.title.y = element_text(color="black", size=14, face="bold")
+ )+theme(axis.text.x = element_text(face="bold", color="black", 
+                                    size=14),
+         axis.text.y = element_text(face="bold", color="black", 
+                                    size=14))

策划这样的事情

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我这里有一些问题

1-你在这里看到，染色体臂的大小，如1p，14q，轮轮太小，太读，甚至颜色导致一些手臂无法读懂。我如何使这些元素的文本大小更大？

2-如何从Y x I (60 and 30 instead of -30 and -60)中移除负号

3-如何将图例标题从Percentage_altered改为Frequency altered，将log10_pvalue更改为-log10(qvalue)？

提前谢谢你

Answer 1

1. geom_repel_text(..., size = 15)
2. 编写一个使用abs的“标记器”函数。 Note：也许你的意思是否定所有，而不是仅仅否定绝对值？在这种情况下，您可以使用`-`而不是abs，也可以使用scale_y_reverse。
3. scale_*_continuous(name="quux", ...)

p <- x %>%
  mutate(
    net_frequency = if_else(CNV == "Deletion", -Percentage_altered/100, Percentage_altered/100),
    log10_pvalue = if_else(CNV == "Deletion", log10_pvalue, log10_pvalue) # ??? kept
  ) %>% 
  ggplot(aes(x = log10_pvalue, y = net_frequency, color = log10_pvalue)) +
  geom_point(aes(size = Percentage_altered)) +
  geom_text_repel(aes(label = gene), size = 15, force = 15) +
  #                                  ^^^^ 1
  geom_hline(yintercept = 0, lty = 2) +
  scale_y_continuous(labels = abs) +
  #                  ^^^^^^ 2
  scale_color_distiller(name = "-log10(qvalue)", type = "div",palette = 5) +
  #                     ^^^^ 3
  scale_size_continuous(name = "Frequency Altered") +
  #                     ^^^^ 3
  theme_classic() +
  facet_wrap(~ group)

p +
  labs(x = "-log10(qvalue)", y = "Net frequency of gain and deletion (%)") +
  theme(
    plot.title = element_text(color="black", size=14, face="bold.italic"),
    axis.title.x = element_text(color="black", size=14, face="bold"),
    axis.title.y = element_text(color="black", size=14, face="bold"),
    axis.text.x = element_text(face="bold", color="black", size=14),
    axis.text.y = element_text(face="bold", color="black", size=14)
  )

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(您需要为您的报告媒体找到一个合适的size=，这里只为强调而夸大。)

顺便说一句，Stack的搜索引擎可以调整，以提供知情的结果。

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Answer 2

以下是对你问题的一些回答。

虽然我不知道你为什么要删除y轴上的减号。

对于geom_tex_repel，你可以玩nudge_..和overlap，你应该看一看幻影的软件包，小插曲这里。

对缩放和legend.title的更改在代码中进行了注释。

也许你可以用理性来回应去除负号的背后。

library(tidyverse)
library(ggrepel)

df %>%
  mutate(
    net_frequency = ifelse(CNV == "Deletion",
      -Percentage_altered / 100, Percentage_altered / 100
    ),
    log10_pvalue = if_else(CNV == "Deletion", log10_pvalue, log10_pvalue)
  ) %>%
  ggplot(aes(x = log10_pvalue, y = net_frequency, color = log10_pvalue)) +
  geom_point(aes(size = Percentage_altered)) +
  # play with nudge and overlap
  geom_text_repel(aes(label = gene), force = 15, nudge_x = 5, max.overlaps = Inf) +
  geom_hline(yintercept = 0, lty = 2) +
  scale_color_distiller(type = "div", palette = 5) +
  # here you can change the tick labels
  scale_y_continuous(
    breaks = seq(-60, 60, 30),
    labels = c("60", "30", "0", "30", "60")
  ) +
  theme_classic() +
  # here you can change title of legend
  guides(size = guide_legend(title = "Frequency altered")) +
  facet_wrap(~group)

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