ggplot2绘制流感血清型月度堆叠柱状图时遇参数缺失类警告

尝试绘制流感血清型按月份统计的堆叠柱状图时，出现以下警告，无法正常生成图表：

Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(diff(sort(x))) : no non-missing arguments to min; returning Inf
4: Removed 7687 rows containing non-finite values (stat_count()).

使用的R代码：

library(tidyverse)
library(dplyr)
library(lubridate)

library(ggplot2)
library(ggthemes)

Sys.setenv(TZ="America/New_York")
today <- Sys.Date()

flu2018_file <- "2018_flu.txt"
df_flu2018 <- as.data.frame(read.table(flu2018_file, sep="\t", header=TRUE, check.names=FALSE, fill=TRUE))

df_flu2018$month <- floor_date(as_date(mdy(df_flu2018$date)), unit="month")

plot_1 <- ggplot(df_flu2018) + 
     geom_histogram(stat="count", aes(x = month, fill = serotype)) 

plot_1

数据集头部的dput输出：

df_flu2018 <- structure(list(accession = c("MH083301", "MH083303", "MH083309", 
"MH083311", "MH081888", "MH081892"), length = c(1752L, 1433L, 
1752L, 1433L, 1441L, 1737L), host = c("Human", "Human", "Human", 
"Human", "Human", "Human"), segment = c("4 (HA)", "6 (NA)", "4 (HA)", 
"6 (NA)", "6 (NA)", "4 (HA)"), serotype = c("H1N1", "H1N1", "H1N1", 
"H1N1", "H3N2", "H3N2"), country = c("USA", "USA", "USA", "USA", 
"USA", "USA"), region = c("N", "N", "N", "N", "N", "N"), date = c("2018/01/02", 
"2018/01/02", "2018/01/03", "2018/01/03", "2018/01/03", "2018/01/03"
), name = c("Influenza A virus (A/Alabama/01/2018(H1N1))", "Influenza A virus (A/Alabama/01/2018(H1N1))", 
"Influenza A virus (A/Alabama/02/2018(H1N1))", "Influenza A virus (A/Alabama/02/2018(H1N1))", 
"Influenza A virus (A/Alabama/03/2018(H3N2))", "Influenza A virus (A/Alabama/03/2018(H3N2))"
), mutations = c("", "", "", "", "", ""), age = c(NA, NA, NA, 
NA, NA, NA), gender = c(NA, NA, NA, NA, NA, NA), lineage = c(NA, 
NA, NA, NA, NA, NA), vac_strain = c(NA, NA, NA, NA, NA, NA), 
    fulllength_plus = c("c", "c", "c", "c", "c", "c"), month = structure(c(NA_real_, 
    NA_real_, NA_real_, NA_real_, NA_real_, NA_real_), class = "Date")), row.names = c(NA, 
6L), class = "data.frame")

从数据集的month列全为NA可以看出，日期转换失败了。你的日期格式是年/月/日（如2018/01/02），但你用了mdy()函数——这个函数是用来解析月/日/年格式的日期，自然无法正确识别，导致生成的month列全部缺失，ggplot找不到有效数据，因此抛出警告并移除所有行。

1. 修正日期转换函数 #

把mdy()替换成ymd()，对应年/月/日的格式：

df_flu2018$month <- floor_date(as_date(ymd(df_flu2018$date)), unit="month")

2. 优化绘图代码（可选） #

如果要绘制堆叠柱状图，用geom_col()配合预先统计好的数据会更直观，也能避免stat_count()的潜在问题：

# 先按月份和血清型统计数量
df_counts <- df_flu2018 %>%
  drop_na(month) %>%  # 移除日期转换失败的行
  count(month, serotype)

# 绘制堆叠柱状图
plot_1 <- ggplot(df_counts, aes(x = month, y = n, fill = serotype)) +
  geom_col(position = "stack") +
  labs(x = "月份", y = "样本数量", fill = "血清型") +
  theme_minimal()

plot_1

验证转换结果 #

运行完日期转换后，可以用head(df_flu2018$month)检查是否生成了正确的月份日期（比如2018-01-01），确认无误后再绘图即可。

内容的提问来源于stack exchange，提问作者Sarah