使用dplyr对因子级别上的理货数据进行排序。

Question

我有一个数据文件df

    structure(list(sample = structure(c(4L, 2L, 1L, 4L, 1L, 2L, 3L, 
3L, 3L, 1L), .Label = c("A1", "B1", "C1", "D2"), class = "factor"), 
    genotype = structure(c(4L, 2L, 2L, 2L, 4L, 4L, 1L, 2L, 3L, 
    1L), .Label = c("germline_private", "germline_recurrent", 
    "somatic_normal", "somatic_tumour"), class = "factor"), n = c(5L, 
    4L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 1L)), class = c("grouped_df", 
"tbl_df", "tbl", "data.frame"), row.names = c(NA, -10L), vars = "sample", drop = TRUE, .Names = c("sample", 
"genotype", "n"), indices = list(c(2L, 4L, 9L), c(1L, 5L), 6:8, 
    c(0L, 3L)), group_sizes = c(3L, 2L, 3L, 2L), biggest_group_size = 3L, labels = structure(list(
    sample = structure(1:4, .Label = c("A1", "B1", "C1", "D2"
    ), class = "factor")), class = "data.frame", row.names = c(NA, 
-4L), vars = "sample", drop = TRUE, .Names = "sample"))

head(df) 

sample event_no           genotype
A1        1     somatic_tumour
A1        2 germline_recurrent
A1        3 germline_recurrent
A1        4     somatic_tumour
A1        5 germline_recurrent
A1        6   germline_private

在本例中，我希望统计每个样本中基因型出现的次数，然后进行排序，以便按照 events的数量对样本进行排序。

我现在拥有的是：

library(tidyverse)

df <- df %>%
  group_by(sample, genotype) %>%
  tally %>%
  arrange(-n)

然后，我想按~基因型绘制每个样本的这些计数：

p <- ggplot(df)
p <- p + geom_histogram(aes(sample, n), stat = "identity")
p <- p + facet_wrap(~genotype)
p

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但是，我希望所有面板中的样本按照右下角图(somatic_tumour)中的计数进行排序。

Answer 1

下面是一种创建new_n的方法，方法是用0替换除somatic_tumour之外的所有somatic_tumour的n，并对2n进行排序，即

library(tidyverse)

df %>% 
 group_by(sample, genotype) %>% 
 tally() %>% 
 mutate(new_n = replace(n, genotype != 'somatic_tumour', 0)) %>% 
 arrange(-new_n, -n) %>% 
 select(-new_n)

这给了，

A tibble: 11x3#组:样本4样本基因型n 1 A1 somatic_tumour 2 2 B1 somatic_tumour 2 3 D2 somatic_tumour 2 4 B1 germline_recurrent 4 5 A1 germline_recurrent 3 6 D2 germline_recurrent 3 C1 germline_private 2 8 C1 germline_recurrent 29 C1 somatic_normal 2 10 A1 germline_private 1 11 D2 somatic_normal 1

Answer 2

您还可以使用left_join来添加每个示例中somatic_tumour出现的次数。之后，使用somatic_tumour观测的somatic_tumour列来创建有序向量。因此，x轴相应地排列。

library(dplyr)
library(ggplot2)
df %>% 
  left_join(df %>% filter(genotype == "somatic_tumour") %>% select(n, sample), 
            by = "sample") %>% 
  arrange(-n.y, -n.x) %>% 
  ungroup() %>% 
  mutate(sample = ordered(sample, 
                          df %>% filter(genotype == "somatic_tumour") %>% 
                            arrange(n) %>% 
                            select(sample) %>% 
                            as_vector(.))) %>% 
  ggplot() + 
  geom_histogram(aes(sample, n.x), stat = "identity") + 
  facet_wrap(~genotype)

注意：这里介绍了NA标签，可能是由于小样本造成的。

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