RStudio绘图窗口加载异常：无法正常显示ASV丰度柱状图

此前可正常运行的phyloseq绘图代码，今日执行后无报错，但绘图窗口无法加载完成，仅角落显示一块灰色区域。已尝试重启R、电脑并重新加载数据，问题仍存在。

相关代码 #

# 基于名为"noMitoChloroMock_physeq"的phyloseq对象开始分析

# 设置对照组样本
control_samples <- c("EB1.11022022", "EB1.11042022", "EB1.11142022", "EB1.11152022", "EB1.11182022", "EB1.11212022", "EB1.12012022", "EB1.12052022", "EB2.11182022", "EB2.12012022", "Pos.control")

# 提取对照组中的分类单元
control_physeq <- noMitoChloroMock_physeq %>% 
  # 筛选对照组样本
  subset_samples(., (names %in% control_samples)) %>% 
  # 移除对照组中丰度为0的ASV
  prune_taxa(taxa_sums(.) > 0, .)

# 获取对照组中的ASV列表
control_ASVs <- data.frame(control_physeq@tax_table)$ASV

#### 对照组ASV分析 ####
# 筛选出数据集中属于对照组的ASV

controlASVs_physeq <- 
  noMitoChloroMock_physeq %>%
  subset_taxa(., ASV %in% control_ASVs)

# 出现问题的绘图代码
controlASVs_physeq %>%
  plot_bar(., "ASV", fill="ASV", facet_grid = Sample_or_Control~.) +
  theme(legend.position = "none",
        axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))

系统环境信息 #

sessionInfo()

R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] decontam_1.20.0 phyloseq_1.44.0 lubridate_1.9.2 forcats_1.0.0   stringr_1.5.0   dplyr_1.1.2     purrr_1.0.1    
 [8] readr_2.1.4     tidyr_1.3.0     tibble_3.2.1    ggplot2_3.4.2   tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] ade4_1.7-22             tidyselect_1.2.0        farver_2.1.1            Biostrings_2.68.1       
 [5] bitops_1.0-7            fastmap_1.1.1           RCurl_1.98-1.12         digest_0.6.31           
 [9] timechange_0.2.0        lifecycle_1.0.3         cluster_2.1.4           survival_3.5-5          
[13] magrittr_2.0.3          compiler_4.3.0          rlang_1.1.1             tools_4.3.0             
[17] igraph_1.4.3            utf8_1.2.3              yaml_2.3.7              data.table_1.14.8       
[21] knitr_1.43              labeling_0.4.2          plyr_1.8.8              withr_2.5.0             
[25] BiocGenerics_0.46.0     grid_4.3.0              stats4_4.3.0            fansi_1.0.4             
[29] multtest_2.56.0         biomformat_1.28.0       colorspace_2.1-0        Rhdf5lib_1.22.0         
[33] scales_1.2.1            iterators_1.0.14        MASS_7.3-60             cli_3.6.1               
[37] rmarkdown_2.22          vegan_2.6-4             crayon_1.5.2            generics_0.1.3          
[41] rstudioapi_0.14         reshape2_1.4.4          tzdb_0.4.0              ape_5.7-1               
[45] rhdf5_2.44.0            zlibbioc_1.46.0         splines_4.3.0           parallel_4.3.0          
[49] BiocManager_1.30.21     XVector_0.40.0          vctrs_0.6.2             Matrix_1.5-4.1          
[53] jsonlite_1.8.5          IRanges_2.34.0          hms_1.1.3               S4Vectors_0.38.1        
[57] foreach_1.5.2           glue_1.6.2              codetools_0.2-19        stringi_1.7.12          
[61] gtable_0.3.3            GenomeInfoDb_1.36.0     munsell_0.5.0           pillar_1.9.0            
[65] htmltools_0.5.5         rhdf5filters_1.12.1     GenomeInfoDbData_1.2.10 R6_2.5.1                
[69] evaluate_0.21           lattice_0.21-8          Biobase_2.60.0          Rcpp_1.0.10             
[73] nlme_3.1-162            permute_0.9-7           mgcv_1.8-42             xfun_0.39               
[77] pkgconfig_2.0.3

解决建议 #

• 直接导出图片到文件：绕过RStudio绘图窗口，用代码直接导出为PDF或PNG，验证绘图逻辑是否正常：

# 导出为PDF
pdf("asv_abundance_plot.pdf", width = 12, height = 8)
print(
  controlASVs_physeq %>%
    plot_bar(., "ASV", fill="ASV", facet_grid = Sample_or_Control~.) +
    theme(legend.position = "none",
          axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
)
dev.off()

# 或导出为PNG
png("asv_abundance_plot.png", width = 1200, height = 800, res = 100)
print(
  controlASVs_physeq %>%
    plot_bar(., "ASV", fill="ASV", facet_grid = Sample_or_Control~.) +
    theme(legend.position = "none",
          axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))
)
dev.off()

• 检查数据完整性：确认controlASVs_physeq的数据是否与之前一致，查看样本数、ASV数量及丰度分布：

dim(controlASVs_physeq)
length(taxa_names(controlASVs_physeq))
summary(taxa_sums(controlASVs_physeq))

• 重置绘图设备：关闭所有打开的绘图设备后重新绘图：

dev.off(dev.list()["RStudioGD"]) # 关闭RStudio绘图窗口
# 重新运行绘图代码
controlASVs_physeq %>%
  plot_bar(., "ASV", fill="ASV", facet_grid = Sample_or_Control~.) +
  theme(legend.position = "none",
        axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1))

• 切换RStudio绘图引擎：打开RStudio的Tools -> Global Options -> General -> Graphics，将Backend从Automatic改为AGG，重启RStudio后再运行代码
• 重装/更新相关包：重装phyloseq和ggplot2，排除包文件损坏的可能：

BiocManager::install("phyloseq", force = TRUE)
install.packages("ggplot2", dependencies = TRUE)

内容的提问来源于stack exchange，提问作者Katie