在 r 中创建 ggplot 抖动图时遇到问题答案

【问题标题】：Trouble creating a ggplot jitter plot in r在 r 中创建 ggplot 抖动图时遇到问题
【发布时间】：2018-02-09 15:08:53
【问题描述】：

我在 R 中创建 ggplot 抖动图时遇到问题。我有一个数据框 aa，并希望用每个基因名称（即 AADAT）标记 x 轴。我希望 y 轴显示倍数变化值（来自 aa 的数值）。另外，我有两个列表，b1 和 b2，其中包含每个基因的一定数量的 TCGA 样本及其倍数变化值。我想根据抖动图中的所有折叠变化值是属于 b1 还是 b2 来为它们着色。我该怎么做？

输入（aa）：

structure(list(TCGA.BC.A10Q = c(2.54076411223946, 1.11243159235432, 
-8.07819965644818), TCGA.DD.A1EB = c(0.437216525767862, 0.461169651797969, 
-1.35226172820141), TCGA.DD.A1EG = c(2.19320501695823, 1.27412886320315, 
-3.46331855085169), TCGA.DD.A1EH = c(3.26575582726209, 1.80298461724572, 
-4.4298527877724), TCGA.DD.A1EI = c(0.606030095793745, -0.0475743042500462, 
-3.03789531487311), TCGA.DD.A3A6 = c(2.92707172081351, 1.0710641387449, 
-4.67961035825927), TCGA.DD.A3A8 = c(0.679951440435414, 0.433630069956858, 
-2.02366124071563), TCGA.ES.A2HT = c(-0.0812955357950507, 1.76935812455138, 
0.236573023675848), TCGA.FV.A23B = c(2.29637640282035, 0.364439713535423, 
-1.94003185763597), TCGA.FV.A3I0 = c(3.196518439057, 1.39220627799838, 
-7.67942521158398), TCGA.FV.A3R2 = c(0.859594276372461, 1.0282030128145, 
0.131890257248429)), .Names = c("TCGA.BC.A10Q", "TCGA.DD.A1EB", 
"TCGA.DD.A1EG", "TCGA.DD.A1EH", "TCGA.DD.A1EI", "TCGA.DD.A3A6", 
"TCGA.DD.A3A8", "TCGA.ES.A2HT", "TCGA.FV.A23B", "TCGA.FV.A3I0", 
"TCGA.FV.A3R2"), row.names = c("ABCC10", "ACBD6", "ACSL1"), class = "data.frame")

输入（b1）：

structure(list(ABCC10 = structure(c(2.19320501695823, 0.859594276372461, 
3.196518439057, 3.26575582726209, 2.29637640282035), .Names = c("TCGA.DD.A1EG", 
"TCGA.FV.A3R2", "TCGA.FV.A3I0", "TCGA.DD.A1EH", "TCGA.FV.A23B"
)), ACBD6 = structure(c(1.80298461724572, 0.433630069956858, 
1.76935812455138, 1.27412886320315, 0.461169651797969), .Names = c("TCGA.DD.A1EH", 
"TCGA.DD.A3A8", "TCGA.ES.A2HT", "TCGA.DD.A1EG", "TCGA.DD.A1EB"
)), ACSL1 = structure(c(-1.94003185763597, -3.46331855085169, 
-3.03789531487311, -4.4298527877724), .Names = c("TCGA.FV.A23B", 
"TCGA.DD.A1EG", "TCGA.DD.A1EI", "TCGA.DD.A1EH"))), .Names = c("ABCC10", 
"ACBD6", "ACSL1"))

输入（b2）：

structure(list(ABCC10 = structure(c(2.54076411223946, 0.437216525767862, 
0.606030095793745, 2.92707172081351, 0.679951440435414, -0.0812955357950507
), .Names = c("TCGA.BC.A10Q", "TCGA.DD.A1EB", "TCGA.DD.A1EI", 
"TCGA.DD.A3A6", "TCGA.DD.A3A8", "TCGA.ES.A2HT")), ACBD6 = structure(c(1.11243159235432, 
-0.0475743042500462, 1.0710641387449, 0.364439713535423, 1.39220627799838, 
1.0282030128145), .Names = c("TCGA.BC.A10Q", "TCGA.DD.A1EI", 
"TCGA.DD.A3A6", "TCGA.FV.A23B", "TCGA.FV.A3I0", "TCGA.FV.A3R2"
)), ACSL1 = structure(c(-8.07819965644818, -1.35226172820141, 
-4.67961035825927, -2.02366124071563, 0.236573023675848, -7.67942521158398, 
0.131890257248429), .Names = c("TCGA.BC.A10Q", "TCGA.DD.A1EB", 
"TCGA.DD.A3A6", "TCGA.DD.A3A8", "TCGA.ES.A2HT", "TCGA.FV.A3I0", 
"TCGA.FV.A3R2"))), .Names = c("ABCC10", "ACBD6", "ACSL1"))

【问题讨论】：

您是否尝试过任何 ggplot 代码？如果是这样，也分享一下。另外，请在reproducible format 等dput() 中分享您的数据，以便更轻松地为您提供帮助。
你试过什么，你能把你的数据存入我们可以方便地使用吗？
这是我试过的代码（我知道这是错误的，我只是不确定如何准确地创建我的情节）：
ggplot(aa, aes(row.names(aa), aa)) + geom_jitter(aes(color = v1))
我刚刚编辑了代码并提供了 dput 值

标签： r ggplot2

【解决方案1】：

你在寻找这样的东西吗？

library(dplyr); library(tidyr); library(ggplot2)

# convert aa from wide to long format
aa$gene <- rownames(aa)
aa <- aa %>%
  gather(TCGA, fold.change, -gene)

# convert lookup lists into data frame for matching
match.table <- rbind(stack(b1) %>% mutate(source = "b1"),
                     stack(b2) %>% mutate(source = "b2"))

aa <- left_join(aa, match.table, 
                by = c("gene" = "ind", "fold.change" = "values"))

ggplot(aa,
       aes(x = gene, y = fold.change, col = source)) +
  geom_jitter() +
  theme_light()

【讨论】：