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tomwenseleers
graph2ppt connection error when exporting Seurat FeaturePlot in R 4.2 Rmarkdown
Dear developer,
Many thanks for the great tool! Very handy. I'll be grateful for your assistance with the issue below.
I updated my rstudio to the latest version and R to 4.2 and now not able to export getting the error 'Warning in .Internal(environment(fun)) : closing unused connection 3 (/var/folders/9h/zbzv_b3j3wz2r6mdgw9s2p04000lw8/T//RtmpkTyPis/filee19561b44ad/raster-rId000002.png) Warning: cannot open file '/var/folders/9h/zbzv_b3j3wz2r6mdgw9s2p04000lw8/T//RtmpkTyPis/filee197fc756a/raster-rId000002.png': No such file or directoryError in open.connection(con, "rb") : cannot open the connection'
I have tried making a reproducible example with the dataset loaded into pbmc found here ( https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz )
The code can be run in rmarkdown as below
title: "export trial" output: html_document date: "2023-01-25"
knitr::opts_chunk$set(echo = TRUE)
library(dplyr)
library(Seurat)
library(export)
# Load the PBMC dataset
pbmc.data <- Read10X(data.dir = "/Users/jr35/Google Drive/My Drive/PHD_documents/trial_datasets/filtered_gene_bc_matrices/hg19/")
# Initialize the Seurat object with the raw (non-normalized data).
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)
pbmc <- FindVariableFeatures(pbmc, selection.method = "vst", nfeatures = 2000)
pbmc <- ScaleData(pbmc)
pbmc <- RunPCA(pbmc, features = VariableFeatures(object = pbmc))
pbmc <- FindNeighbors(pbmc, dims = 1:10)
pbmc <- FindClusters(pbmc, resolution = 0.5)
pbmc <- RunUMAP(pbmc, dims = 1:10)
Plotting and exporting
FeaturePlot(pbmc, features = "CCR7", dims = c(1,2), pt.size = 1.5, label = T, label.size = 5, repel = T)
graph2ppt(file = '/Users/jr35/Google Drive/My Drive/PHD_documents/test_exp.ppt')
The output of session info is below
sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gdtools_0.3.0 export_0.3.0 patchwork_1.1.2 SeuratObject_4.1.3 Seurat_4.3.0 dplyr_1.0.10
loaded via a namespace (and not attached):
[1] utf8_1.2.2 spatstat.explore_3.0-5 reticulate_1.27 tidyselect_1.2.0
[5] RSQLite_2.2.20 AnnotationDbi_1.60.0 htmlwidgets_1.6.1 grid_4.2.2
[9] BiocParallel_1.32.5 Rtsne_0.16 scatterpie_0.1.8 munsell_0.5.0
[13] codetools_0.2-18 ica_1.0-3 future_1.30.0 miniUI_0.1.1.1
[17] withr_2.5.0 spatstat.random_3.1-3 colorspace_2.1-0 GOSemSim_2.24.0
[21] progressr_0.13.0 Biobase_2.58.0 uuid_1.1-0 knitr_1.42
[25] rstudioapi_0.14 stats4_4.2.2 SingleCellExperiment_1.20.0 ROCR_1.0-11
[29] officer_0.5.1 tensor_1.5 DOSE_3.25.0.002 listenv_0.9.0
[33] labeling_0.4.2 MatrixGenerics_1.10.0 GenomeInfoDbData_1.2.9 polyclip_1.10-4
[37] bit64_4.0.5 farver_2.1.1 pheatmap_1.0.12 downloader_0.4
[41] treeio_1.22.0 parallelly_1.34.0 vctrs_0.5.2 generics_0.1.3
[45] gson_0.0.9 xfun_0.36 qpdf_1.3.0 R6_2.5.1
[49] GenomeInfoDb_1.34.6 graphlayouts_0.8.4 bitops_1.0-7 spatstat.utils_3.0-1
[53] cachem_1.0.6 reshape_0.8.9 fgsea_1.24.0 gridGraphics_0.5-1
[57] DelayedArray_0.24.0 assertthat_0.2.1 promises_1.2.0.1 scales_1.2.1
[61] ggraph_2.1.0 enrichplot_1.19.1.991 gtable_0.3.1 globals_0.16.2
[65] goftest_1.2-3 tidygraph_1.2.2 rlang_1.0.6 systemfonts_1.0.4
[69] splines_4.2.2 lazyeval_0.2.2 broom_1.0.3 spatstat.geom_3.0-5
[73] rgl_1.0.1 yaml_2.3.7 reshape2_1.4.4 abind_1.4-5
[77] backports_1.4.1 httpuv_1.6.8 qvalue_2.30.0 clusterProfiler_4.7.0
[81] tools_4.2.2 ggplotify_0.1.0 ggplot2_3.4.0 ellipsis_0.3.2
[85] RColorBrewer_1.1-3 BiocGenerics_0.44.0 stargazer_5.2.3 ggridges_0.5.4
[89] devEMF_4.2 Rcpp_1.0.10 plyr_1.8.8 base64enc_0.1-3
[93] zlibbioc_1.44.0 purrr_1.0.1 RCurl_1.98-1.9 openssl_2.0.5
[97] deldir_1.0-6 pbapply_1.7-0 viridis_0.6.2 cowplot_1.1.1
[101] S4Vectors_0.36.1 zoo_1.8-11 SummarizedExperiment_1.28.0 ggrepel_0.9.2
[105] cluster_2.1.4 crul_1.3 magrittr_2.0.3 data.table_1.14.6
[109] scattermore_0.8 openxlsx_4.2.5.1 flextable_0.8.4 lmtest_0.9-40
[113] RANN_2.6.1 fitdistrplus_1.1-8 matrixStats_0.63.0 mime_0.12
[117] evaluate_0.20 xtable_1.8-4 HDO.db_0.99.1 readxl_1.4.1
[121] IRanges_2.32.0 gridExtra_2.3 compiler_4.2.2 tibble_3.1.8
[125] shadowtext_0.1.2 KernSmooth_2.23-20 crayon_1.5.2 htmltools_0.5.4
[129] ggfun_0.0.9 later_1.3.0 tidyr_1.3.0 aplot_0.1.9
[133] DBI_1.1.3 tweenr_2.0.2 MASS_7.3-58.2 Matrix_1.5-3
[137] cli_3.6.0 parallel_4.2.2 igraph_1.3.5 GenomicRanges_1.50.2
[141] pkgconfig_2.0.3 sp_1.6-0 plotly_4.10.1 spatstat.sparse_3.0-0
[145] xml2_1.3.3 ggtree_3.6.2 XVector_0.38.0 rvg_0.3.2
[149] yulab.utils_0.0.6 stringr_1.5.0 digest_0.6.31 sctransform_0.3.5
[153] RcppAnnoy_0.0.20 httpcode_0.3.0 spatstat.data_3.0-0 Biostrings_2.66.0
[157] rmarkdown_2.20 cellranger_1.1.0 leiden_0.4.3 fastmatch_1.1-3
[161] tidytree_0.4.2 uwot_0.1.14 curl_5.0.0 shiny_1.7.4
[165] lifecycle_1.0.3 nlme_3.1-161 jsonlite_1.8.4 askpass_1.1
[169] viridisLite_0.4.1 fansi_1.0.4 pillar_1.8.1 lattice_0.20-45
[173] GGally_2.1.2 KEGGREST_1.38.0 fastmap_1.1.0 httr_1.4.4
[177] survival_3.5-0 GO.db_3.16.0 glue_1.6.2 zip_2.2.2
[181] png_0.1-8 bit_4.0.5 ggforce_0.4.1 stringi_1.7.12
[185] blob_1.2.3 gfonts_0.2.0 pdftools_3.3.2 memoise_2.0.1
[189] irlba_2.3.5.1 future.apply_1.10.0 ape_5.6-2
Hmm thanks for the bug report. I can confirm that
library(Seurat)
data("pbmc_small")
pl = FeaturePlot(object = pbmc_small, features = 'PC_1')
graph2ppt(x=pl, file="./test.pptx", width=7, height=5)
also produces the error
Error in open.connection(con, "rb") : cannot open the connection
In addition: Warning message:
In open.connection(con, "rb") :
cannot open file 'C:\Users\bherr\AppData\Local\Temp\RtmpCQqwZP\file1f6849f02517/raster-rId000002.png': No such file or directory
for me - haven't figured out yet where that is coming from...
graph2doc(x=pl, file="./test.docx", width=7, height=5)
does seem to work though, if that's of any help...
Will try to look a bit further where this is coming from...
I have the similar problem, and I have just updated all my R CRAN packages 3 hours ago. But I found that the ggplot object (like plots made through ggsurvplot() and ggplot2() function ) works fine, but the plotsI build through dotplot() function using the enrichr package for enrichment analysis got the error. I hope my experience will help to find the bug.
> ggsurvplot(fit, data = lung)
> export::graph2ppt(file = './output/test.pptx',append=T)
Exported graph as ./output/test.pptx
> ggplot(df, aes(gp, y)) +
+ geom_point()
> export::graph2ppt(file = './output/test.pptx',append=T)
Exported graph as ./output/test.pptx
> dotplot(Case_go)
> export::graph2ppt(file = './output/test.pptx',append=T)
Error in open.connection(con, "rb") : cannot open the connection
In addition: Warning message:
In open.connection(con, "rb") :
cannot open file 'C:\Users\JinXing\AppData\Local\Temp\RtmpMTp2kQ\file2bb8508d12e7/raster-rId000002.png': No such file or directory
Help!!! I also suffered the same problem.
Error in open.connection(con, "rb") : cannot open the connection In addition: Warning message: In open.connection(con, "rb") : cannot open file 'C:\Users\yaolq\AppData\Local\Temp\Rtmpu4jUEU\filecf8430fca3/raster-rId000002.png': No such file or directory
Hope some can find the solutions, really thanks.
