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r - 如何使用 ggsignif 包将 p 值添加到堆积条形图？

问题描述

我试图使用 ggsignif 包将重要的 p 值添加到多面堆积条形图中，但收到一条错误消息

check_factor(f) 中的错误：找不到对象“等级”

非常感谢任何有关如何解决此问题的建议！以下是重现我的问题的数据和代码：

library(tidyverse) 
library(cowplot) 
#> 
#> Attaching package: 'cowplot'
#> The following object is masked from 'package:ggplot2':
#> 
#>     ggsave
library(ggsignif) 

# Make a dataframe for plotting stacked bar plot
df <- data.frame(Diet = rep(c("REF", "IM"), each = 8),
                 Variable = c("hpv", "hpv", "hpv", "hpv", "smc", "smc", "lpc", "lpc",
                              "hpv", "hpv", "hpv", "smc", "smc", "smc", "lpc", "lpc"),
                 Rank = c("Mild", "Moderate", "Marked", "Severe", "Normal", "Mild", "Normal", "Mild",
                          "Mild", "Moderate", "Marked", "Normal", "Mild", "Moderate", "Normal", "Mild"),
                 Percent = c(5.56, 38.9, 44.4, 11.1, 38.9, 61.1, 77.8, 22.2, 
                             16.7, 66.7, 16.7, 11.1, 72.2, 16.7, 50, 50)
                 )

# Specify the desired orders of factors and convert "Rank" to an ordered factor
df$Diet <- factor(df$Diet, levels = c("REF", "IM"))
df$Variable <- factor(df$Variable, levels = c("hpv", "smc", "lpc"))
df$Rank <- ordered(df$Rank, levels = c("Normal", "Mild", "Moderate", "Marked", "Severe")) # Rank as ordered factor

# Define color scheme 
my_col = c(Normal = "royalblue2", Mild = "peachpuff1", Moderate = "tan1", Marked = "tomato", Severe = "red3")

# Make stacked barplot 
p <- ggplot(df, aes(Diet, Percent, fill = forcats::fct_rev(Rank))) + # forcats::fct_rev() reverses stacked bars
  geom_bar(stat = "identity") +
  facet_wrap(~ Variable, nrow = 1) +
  scale_fill_manual(values = my_col) + 
  scale_y_continuous(limits = c(0, 105), breaks = 0:5*20, expand = expand_scale(mult = c(0, 0.05))) +
  labs(title = "Stacked bar plot", y = "%") +
  guides(fill = guide_legend(title = "Rank")) + 
  theme_cowplot()

# Make a datafraome for p value annotation
anno <- data.frame(Variable = "hpv",
                   p = 0.03,
                   start = "REF",
                   end = "IM",
                   y = 102)

# Add p value to the plot
p + geom_signif(data = anno,
                aes(xmin = start, 
                    xmax = end, 
                    annotations = p, 
                    y_position = y),
                textsize = 4, 
                tip_length = 0,
                manual = TRUE)
#> Warning: Ignoring unknown aesthetics: xmin, xmax, annotations, y_position
#> Error in check_factor(f): object 'Rank' not found

标签： rggplot2

解决方案

你可以试试

p <- ggplot(df, aes(Diet, Percent, fill = Rank)) + 
  geom_col() +
  facet_wrap(~ Variable) +
  geom_signif(annotations = 0.03, y_position = 105 ,xmin="IM", xmax="REF")
p

在此处输入图像描述

在另一个方面添加注释，您必须使用此处的代码对绘图背后的数据进行硬编码如何注释 R 上每个方面（条形图）的不同值？

p <- ggplot_build(p)
p$data[[2]] <- rbind(p$data[[2]],p$data[[2]]) # rbind a second annotation a three rows
p$data[[2]]$PANEL[4:6] <- 2 # panel 2
p$data[[2]]$annotation[4:6] <- "your text" 
plot(ggplot_gtable(p))

在此处输入图像描述

我用过ggsignif_0.4.0&ggplot2_3.0.0 数据

df <- data.frame(Diet = rep(c("REF", "IM"), each = 8),
                 Variable = c("hpv", "hpv", "hpv", "hpv", "smc", "smc", "lpc", "lpc",
                              "hpv", "hpv", "hpv", "smc", "smc", "smc", "lpc", "lpc"),
                 Rank = c("Mild", "Moderate", "Marked", "Severe", "Normal", "Mild", "Normal", "Mild",
                          "Mild", "Moderate", "Marked", "Normal", "Mild", "Moderate", "Normal", "Mild"),
                 Percent = c(5.56, 38.9, 44.4, 11.1, 38.9, 61.1, 77.8, 22.2, 
                             16.7, 66.7, 16.7, 11.1, 72.2, 16.7, 50, 50)
                 )

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