在ggplot中使用Apply函数来绘制数据框列的子集 [英] Using apply functions with ggplot to plot a subset of dataframe columns

问题描述

我有一个包含许多列的数据框 df ...我想绘制列子集的图，其中 c 是我要绘制的列的列表.

I have a dataframe df with many columns ... I'd like plot of subset of columns where c is a list of the columns I'd like to plot.

我当前正在执行以下操作

I'm currently doing the following

df <-structure(list(Image.Name = structure(1:5, .Label = c("D1C1", "D2C2", "D4C1", "D5C3", "D6C2"), class = "factor"), Experiment = structure(1:5, .Label = c("020718 perfusion EPC_BC_HCT115_Day 5", "020718 perfusion EPC_BC_HCT115_Day 6", "020718 perfusion EPC_BC_HCT115_Day 7", "020718 perfusion EPC_BC_HCT115_Day 8", "020718 perfusion EPC_BC_HCT115_Day 9"), class = "factor"), Type = structure(c(2L, 1L, 1L, 2L, 1L), .Label = c("VMO", "VMT"), class = "factor"), Date = structure(c(1L, 1L, 1L, 1L, 1L), .Label = "18-Apr-18", class = "factor"), Time = structure(1:5, .Label = c("12:42:02 PM", "12:42:29 PM", "12:42:53 PM", "12:43:44 PM", "12:44:23 PM"), class = "factor"),     Low.Threshold = c(10L, 10L, 10L, 10L, 10L), High.Threshold = c(255L,     255L, 255L, 255L, 255L), Vessel.Thickness = c(7L, 7L, 7L,     7L, 7L), Small.Particles = c(0L, 0L, 0L, 0L, 0L), Fill.Holes = c(0L,     0L, 0L, 0L, 0L), Scaling.factor = c(0.001333333, 0.001333333,     0.001333333, 0.001333333, 0.001333333), X = c(NA, NA, NA,     NA, NA), Explant.area = c(1.465629333, 1.093447111, 1.014612444,     1.166950222, 1.262710222), Vessels.area = c(0.255562667,     0.185208889, 0.195792, 0.153907556, 0.227996444), Vessels.percentage.area = c(17.43706003,     16.93807474, 19.29722044, 13.18887067, 18.05611774), Total.Number.of.Junctions = c(56L,     32L, 39L, 18L, 46L), Junctions.density = c(38.20884225, 29.26524719,     38.43832215, 15.42482246, 36.42957758), Total.Vessels.Length = c(12.19494843,     9.545333135, 10.2007416, 7.686755647, 11.94211976), Average.Vessels.Length = c(0.182014156,     0.153956986, 0.188902622, 0.08938088, 0.183724919), Total.Number.of.End.Points = c(187L,     153L, 145L, 188L, 167L), Average.Lacunarity = c(0.722820111,     0.919723402, 0.86403871, 1.115896082, 0.821753818)), .Names = c("Image.Name", "Experiment", "Type", "Date", "Time", "Low.Threshold", "High.Threshold", "Vessel.Thickness", "Small.Particles", "Fill.Holes", "Scaling.factor", "X", "Explant.area", "Vessels.area", "Vessels.percentage.area", "Total.Number.of.Junctions", "Junctions.density", "Total.Vessels.Length", "Average.Vessels.Length", "Total.Number.of.End.Points", "Average.Lacunarity"), row.names = c(NA, -5L), class = "data.frame")


doBarPlot <- function(x) {
  p <- ggplot(x, aes_string(x="Type", y=colnames(x), fill="Type") ) +
    stat_summary(fun.y = "mean", geom = "bar", na.rm = TRUE) +
    stat_summary(fun.data = "mean_cl_normal", geom = "errorbar", width=0.5, na.rm = TRUE) +
    ggtitle("VMO vs. VMT") +
    theme(plot.title = element_text(hjust = 0.5) )
  print(p)
  ggsave(sprintf("plots/%s_bars.pdf", colnames(x) ) )
  return(p)
}

c = c('Total.Vessels.Length', 'Total.Number.of.Junctions', 'Total.Number.of.End.Points', 'Average.Lacunarity')
p[c] <- lapply(df[c], doBarPlot)

但是这会产生以下错误:

However this yields the following error :

Error: ggplot2 doesn't know how to deal with data of class numeric

调试表明，doBarPlot内的 x 类型为数字，而不是 data.frame ，因此 ggplot 错误.但是， test<-df2 [c] 产生类型为 data.frame 的变量.

Debugging shows that x inside of doBarPlot is of the type numeric rather than data.frame, so ggplot errors. However, test <- df2[c] yields a variable of the type data.frame.

为什么 x 是数字?在不求助于循环的情况下应用 doBarPlot 的最佳方法是什么?

Why is x a numeric? What's the best way to apply doBarPlot without resorting to a loop?

推荐答案

正如其他人所指出的那样，您最初的方法存在的问题是，当您在数据帧上使用 lapply 时，您所需要的元素迭代的将是列向量，而不是1列数据帧.但是，即使您对1列数据帧进行了迭代，您的函数也会失败:提供给 ggplot 调用的数据帧将不包含您所需要的 Type 列在情节中使用.

As others have noted, the problem with your initial approach is that when you use lapply on a data frame, the elements that you are iterating over will be the column vectors, rather than 1-column data frames. However, even if you did iterate over 1-column data frames, your function would fail: the data frame supplied to the ggplot call wouldn't contain the Type column that you use in the plot.

相反，您可以将函数修改为带有两个参数:完整的数据框和要在y轴上使用的列的名称.

Instead, you could modify the function to take two arguments: the full data frame, and the name of the column that you want to use on the y-axis.

doBarPlot <- function(data, y) {
  p <- ggplot(data, aes_string(x = "Type", y = y, fill = "Type")) +
    stat_summary(fun.y = "mean", geom = "bar", na.rm = TRUE) +
    stat_summary(
      fun.data = "mean_cl_normal",
      geom = "errorbar",
      width = 0.5,
      na.rm = TRUE
    ) +
    ggtitle("VMO vs. VMT") +
    theme(plot.title = element_text(hjust = 0.5))
  print(p)
  ggsave(sprintf("plots/%s_bars.pdf", y))
  return(p)
}

然后，您可以使用 lapply 遍历要绘制的列的字符向量，同时通过 ... 作为固定参数来提供数据框到您的绘图功能:

Then, you can use lapply to iterate over the character vector of columns you want to plot, while supplyig the data frame via the ... as a fixed argument to your plotting function:

library(ggplot2)

cols <- c('Total.Vessels.Length', 'Total.Number.of.Junctions',
          'Total.Number.of.End.Points', 'Average.Lacunarity')
p <- lapply(cols, doBarPlot, data = df)

此外，如果您不介意将所有绘图放在一个文件中，则还可以使用 tidyr :: gather 将数据重整为长格式，然后使用 facet_wrap (如@RichardTelford在他的评论中所建议)，避免了迭代并完全不需要函数:

Further, if you don't mind having all of the plots in one file, you could also use tidyr::gather to reshape your data into long form, and use facet_wrap in your plot (as suggested by @RichardTelford in his comment), avoiding the iteration and the need for a function altogether:

library(tidyverse)

df %>% 
  gather(variable, value, cols) %>% 
  ggplot(aes(x = Type, y = value, fill = Type)) +
    facet_wrap(~ variable, scales = "free_y") +
    stat_summary(fun.y = "mean", geom = "bar", na.rm = TRUE) +
    stat_summary(
      fun.data = "mean_cl_normal",
      geom = "errorbar",
      width = 0.5,
      na.rm = TRUE
    ) +
    ggtitle("VMO vs. VMT") +
    theme(plot.title = element_text(hjust = 0.5))

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