ggplot2保存TIFF格式绘图失败问题求助

问题描述 #

用ggplot2绘制完成g3后，RStudio能正常预览，但调用tiff()函数保存TIFF文件时提示无法打开文件；改用ggsave()函数也出现错误。

报错详情 #

使用tiff()函数的报错 #

执行代码：

tiff("CREATINE** fit dot plot Day 2 and 4", width=6, height=6, units='in', res=1080, compression = 'none')
plot(g3)
print(g3)
dev.off()

控制台输出：

tiff("CREATINE** fit dot plot Day 2 and 4", width=6, height=6, units='in', res=1080, compression = 'none')
plot(g3)
# `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
print(g3)
# TIFFOpen: CREATINE** fit dot plot Day 2 and 4: Cannot open.
# `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
# Warning message:
# In grid.newpage() :
#   unable to open TIFF file 'CREATINE** fit dot plot Day 2 and 4'
dev.off()
# TIFFOpen: CREATINE** fit dot plot Day 2 and 4: Cannot open.
# RStudioGD 
#         2 
# Warning message:
# In dev.off() :
#   unable to open TIFF file 'CREATINE** fit dot plot Day 2 and 4'

使用ggsave()函数的报错 #

执行代码：

ggsave("CREATINE** fit dot plot Day 2 and 4", width=6, height=6, units='in', res=1080, compression = 'none')

报错信息：

# Error in `ggsave()`:
# ! `filename` has no file extension and `device` is "NULL".
# Run `rlang::last_trace()` to see where the error occurred.
rlang::last_trace()
# <error/rlang_error>
# Error in `ggsave()`:
# ! `filename` has no file extension and `device` is "NULL".
# ---
# Backtrace:
#     ▆
#  1. └─ggplot2::ggsave(...)
# Run rlang::last_trace(drop = FALSE) to see 3 hidden frames.

完整绘图代码 #

Sys.time()
[1] "2024-02-14 13:37:07 MST"
day_2<-subset(Merged.Master.File_5.24.22_circ, Study.Day==2)
day_4<-subset(Merged.Master.File_5.24.22_circ, Study.Day==4)

library(ggplot2); library(lme4)
theme_new <- theme_set(theme_classic())
theme_new <- theme_update(text = element_text(colour="black", size = 15, family="sans"))
theme_new <- theme_update(legend.position = "top", legend.text = element_text(colour="black", size = 14), legend.title=element_blank(), plot.margin=unit(c(0,0,0,0),"mm"))
theme_set(theme_new)

day2_DFM <- lmer(CREATINE~cos((2*pi*Time)/24) + sin((2*pi*Time)/24) + (1|Subject), data=day_2, REML=F, na.action=na.omit)
day4_DFM <- lmer(CREATINE~cos((2*pi*Time)/24) + sin((2*pi*Time)/24) + (1|Subject), data=day_4, REML=F, na.action=na.omit)
###not sure how important these 2 lines are###
FittedFE.D2 <- function(day2_DFM) model.matrix(day2_DFM) %*% fixef(day2_DFM)
head(FittedFE.D2(day2_DFM))

plotdata.D2 <- data.frame(day2_DFM@frame, fitted = FittedFE.D2(day2_DFM))
plotdata.D2$Time <- day_2$Time
FittedFE.D4 <- function(day4_DFM) model.matrix(day4_DFM) %*% fixef(day4_DFM)
plotdata.D4 <- data.frame(day4_DFM@frame, fitted = FittedFE.D4(day4_DFM))
plotdata.D4$Time <- day_4$Time
myY <- scale_y_continuous(name = "Creatine (DFM)")
myX <- scale_x_continuous(breaks=c(1,5,9,13,17,21), name = "Relative Clock Hour")
plotdata <- rbind(plotdata.D2, plotdata.D4)

plotdata$day<-Merged.Master.File_5.24.22_circ$Study.Day
g1 <- ggplot(data=plotdata,aes(y= CREATINE, x=Time)) + stat_summary(aes(y=CREATINE, group=day, colour=factor(day)), fun=mean, geom="point", size=2, shape=16) + myX + myY + scale_color_manual(values=c("black", "red"), labels=c("Baseline", "Circadian Misalignment")) + theme(legend.title = element_blank()) + theme(legend.position = "top")
print(g1)
plotdata$SEM.hi <- Merged.Master.File_5.24.22_circ$SEM.hi
plotdata$SEM.lo <- Merged.Master.File_5.24.22_circ$SEM.lo
g2 <- g1 + geom_errorbar(data=plotdata, aes(ymin=SEM.lo, ymax=SEM.hi, group=day, colour=factor(day)), width=0.3)
print(g2)
g3 <- g2 + stat_smooth(aes(y=fitted, group=plotdata$day, colour=factor(plotdata$day)), span=0.9, geom="line", linetype=1, lwd=1, se=F) +  coord_cartesian(ylim = c(-0.5, 0.5))
print(g3)
tiff("CREATINE** fit dot plot Day 2 and 4", width=6, height=6, units='in', res=1080, compression = 'none')
plot(g3)
print(g3)
dev.off()

解决方案 #

问题根源 #

1. 文件名含非法字符：文件名中的**是系统禁止的特殊字符，导致tiff()无法创建文件；
2. ggsave缺少扩展名：ggsave需要明确的.tiff扩展名来识别输出设备，无扩展名时会报错。

修复步骤 #

方法1：修正tiff()函数的调用

移除文件名中的特殊字符，添加.tiff扩展名，同时ggplot对象只需调用print()即可：

tiff("CREATINE_fit_dot_plot_Day_2_and_4.tiff", width=6, height=6, units='in', res=1080, compression = 'none')
print(g3)
dev.off()

方法2：正确使用ggsave()

添加.tiff扩展名，可指定device = tiff确保格式正确：

ggsave("CREATINE_fit_dot_plot_Day_2_and_4.tiff", plot = g3, width=6, height=6, units='in', res=1080, compression = 'none', device = tiff)

额外注意事项 #

• 文件名避免使用*、/、:等系统保留字符；
• 确认当前工作目录有写入权限，可通过getwd()查看目录，setwd()切换目录；
• ggplot对象无需调用plot()，仅用print()输出到绘图设备即可，重复调用会导致重复绘图。

内容的提问来源于stack exchange，提问作者misia