在 r 中按列添加平均线组

Question

嗨，我有这样的数据：

总共 38 列。治疗列中有 10 种治疗类型，日期列数据示例代码中的日期为 25-29（示例为 2 种治疗类型，但数据有 10 种类型）：

df <- structure(
    list(
      Christensenellaceae = c(
        0,
        0.009910731,
        0.010131195,
        0.009679938,
        0.01147601,
        0.010484508,
        0.008641566,
        0.010017172,
        0.010741488,
        0.1,
        0.2,
        0.3,
        0.4),
      Date=c(25,25,25,25,25,27,27,27,27,27,27,27,27),
      Treatment = c(
        "Original Sample",
        "Original Sample",
        "Original Sample",
        "Original Sample",
        "Original Sample"
        "Treatment 1",
        "Treatment 1",
        "Treatment 1",
        "Treatment 1",
        "Treatment 2",
        "Treatment 2",
        "Treatment 2",
        "Treatment  2")
    ),class = "data.frame",
    row.names = c(NA,-9L)
  )

我想做的是为每一列创建 2 个图，一个用于原始处理，另一个用于此处示例 (1-2) 中的所有处理类型 (1-10)，并添加观察的平均线基于每种治疗类型。治疗区总共应该有 10 条平均线（这里是 2 条）。遗憾的是我不明白如何添加按治疗类型分组的行这是我基于所有治疗类型的一行代码。我如何添加按治疗类型分组的行：

df_3 %>% 
  pivot_longer(-treatment) %>% 
  mutate(plot = ifelse(str_detect(treatment, "Original"), 
                       "Original sample", 
                       "Treatment"),
         treatment = str_extract(treatment, "\d+$")) %>% 
  group_by(name) %>% 
  group_split() %>% 
  map(~.x %>% ggplot(aes(x = factor(treatment), y = value, color = factor(name))) +
        geom_point() +
        stat_summary(aes(y = value,group=1), fun.y=mean, colour="red", geom="line",group=1)
        +
        facet_wrap(~plot, scales = "free_x") +
        labs(x = "Treatment", y = "Value", color = "Taxa") +
        guides(x =  guide_axis(angle = 90))+
        theme_bw())

如您所见，只有一条平均线，每种治疗类型我需要 10 条（此处为 2 条）。有什么办法可以编辑我的代码使其正常工作吗？谢谢:)

我也试过这段代码，但我似乎没有用

      df %>% 
     pivot_longer(-c(Treatment, Date), names_to = "taxon") 
      %>% mutate( type = Treatment %>% str_detect("Original") 
      %>% ifelse("Original", "Treatment"), treatment_nr = Treatment 
       %>% str_extract("(?<=Treatment )[0-9]+") )
         %>% ggplot(aes(Date, value, color = treatment_nr)) + 
           geom_point() + stat_summary( geom = "point", fun.y = 
           "mean", size = 3, shape = 24 ) + geom_line() + facet_grid(type 
            ~ taxon, scales = "free_y") #> Warning: `fun.y` is deprecated. 
                Use `fun` instead.

Answer 1

您的数据格式不正确，并且与您的原始示例代码不匹配（例如 Treatment 而不是 treatment）。无论如何，我将在这里生成一些数据，以便根据您的图像中的数据说明解决方案。

library(tidyverse)
set.seed(1)
df <-
  data.frame(
    Christensenellaceae = runif(105),
    treatment = rep(c("Original Sample_25", 
                      paste0("Treatment", 1:10, "_", 27), 
                      paste0("Treatment", 1:10, "_", 28)), 
                    each = 5)
  )

因为您将平均值生成为一条线，所以它将连接在 x 轴上。我做了一个非常懒惰的工作，使用一个片段并在绘图之前计算平均值。根据您的十次治疗的外观，您可以通过更改 avg_line_length.

来更改平均线的大小

因为该段还有额外的 x 轴值（例如 0.65、1.35），x 轴将默认包含这些额外值。我已经创建了标签和中断来解决这个问题，并且为此使用了中间数据 labs_df。我把原来的留空了。您可以使用 color/linetype 来在图例中也将行显示为 'Mean'。

avg_line_length <- 0.35

p <-
  df %>% 
    pivot_longer(-treatment) %>% 
    mutate(plot = ifelse(str_detect(treatment, "Original"), 
                         "Original sample", 
                         "Treatment"),
           treatment = as.numeric(str_extract(treatment, "\d+")),
           treatment_label = ifelse(plot %in% "Original sample", "", treatment)) %>% 
    {. ->> lab_df} %>%
    group_by(treatment) %>%
    mutate(avg = mean(value),
           xstart = treatment - avg_line_length,
           xend = treatment + avg_line_length) %>%
    ungroup() %>%
    group_by(name) %>%
    group_split() %>% 
    map(~.x %>% ggplot() +
          geom_point(aes(x = treatment, y = value, color = name)) +
          geom_segment(aes(x = xstart, xend = xend, y = avg, yend = avg, color = name)) +
          scale_x_continuous(breaks = lab_df$treatment, labels = lab_df$treatment_label) +
          facet_wrap(~plot, scales = "free_x") +
          labs(x = "Treatment", y = "Value", color = "Taxa") +
          guides(x =  guide_axis(angle = 90))+
          theme_bw()) 

p
#> [[1]]

如果您不想要原始样本的平均线，只需额外 ifelse.

p2 <-
  df %>% 
    pivot_longer(-treatment) %>% 
    mutate(plot = ifelse(str_detect(treatment, "Original"), 
                         "Original sample", 
                         "Treatment"),
           treatment = as.numeric(str_extract(treatment, "\d+")),
           treatment_label = ifelse(plot %in% "Original sample", "", treatment)) %>% 
    {. ->> lab_df} %>%
    group_by(treatment) %>%
    mutate(avg = ifelse(plot %in% "Original sample", NA, mean(value)),
           xstart = treatment - avg_line_length,
           xend = treatment + avg_line_length) %>%
    ungroup() %>%
    group_by(name) %>%
    group_split() %>% 
    map(~.x %>% ggplot() +
          geom_point(aes(x = treatment, y = value, color = factor(name))) +
          geom_segment(aes(x = xstart, xend = xend, y = avg, yend = avg), colour="red") +
          scale_x_continuous(breaks = lab_df$treatment, labels = lab_df$treatment_label) +
          facet_wrap(~plot, scales = "free_x") +
          labs(x = "Treatment", y = "Value", color = "Taxa") +
          guides(x =  guide_axis(angle = 90))+
          theme_bw()) 

p2
#> [[1]]
#> Warning: Removed 5 rows containing missing values (geom_segment).

内容很乱，但希望能解决您的问题。

在 r 中按列添加平均线组

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