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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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Saving Figures as PDF #587

Closed mhulke closed 1 year ago

mhulke commented 1 year ago

Hello sqjin,

I was hoping you could offer some advice for saving plots from the main analysis. I have read through the many posts regarding how to save a figure, but none of the solutions seem to work. I noticed that most functions output an image as recordedplot, and I haven't been able to find anything online about saving a recordedplot as a pdf. I attempted to convert the recordedplot to a ggplot class, but the function as.grob() gives as error that 'as.grob' doesn't work on the class recordedplot. Similarly, I was not able to save any plots using ggsave (as is done in the tutorial) since the images aren't ggplot class. When I try using pdf() devoff() or svglite() dev.off() using the code:

pdf('test_plot.pdf') netVisual_circle(cellchat@net$count, vertex.weight = groupSize, weight.scale = T, label.edge= F, title.name = "Number of Interactions") dev.off()

I get the following error: ERROR while rich displaying an object: Error in file(con, "rb"): cannot open the connection

Traceback:

  1. tryCatch(withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[mime] . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler), error = outer_handler)
  2. tryCatchList(expr, classes, parentenv, handlers)
  3. tryCatchOne(expr, names, parentenv, handlers[[1L]])
  4. doTryCatch(return(expr), name, parentenv, handler)
  5. withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[mime] . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler)
  6. repr::mime2repr[mime]
  7. repr_png.recordedplot(obj)
  8. repr_recordedplot_generic(obj, ".png", TRUE, dev.cb)
  9. readBin(tf, raw(), file.info(tf)$size)
  10. file(con, "rb") ERROR while rich displaying an object: Error in file(con, "rb"): cannot open the connection

Traceback:

  1. tryCatch(withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[mime] . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler), error = outer_handler)
  2. tryCatchList(expr, classes, parentenv, handlers)
  3. tryCatchOne(expr, names, parentenv, handlers[[1L]])
  4. doTryCatch(return(expr), name, parentenv, handler)
  5. withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[mime] . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler)
  6. repr::mime2repr[mime]
  7. repr_jpg.recordedplot(obj)
  8. repr_recordedplot_generic(obj, ".jpg", TRUE, dev.cb)
  9. readBin(tf, raw(), file.info(tf)$size)
  10. file(con, "rb")

I am working in an R notebook in app.terra. My session information: R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] forcats_1.0.0 stringr_1.5.0 purrr_1.0.1
[4] readr_2.1.3 tidyr_1.3.0 tibble_3.2.1
[7] tidyverse_1.3.2 ggraph_2.1.0 ggplotify_0.1.0
[10] svglite_2.1.1 reticulate_1.28 circlize_0.4.16
[13] patchwork_1.1.2 CellChat_1.6.1 Biobase_2.58.0
[16] BiocGenerics_0.44.0 ggplot2_3.4.2 igraph_1.4.1
[19] dplyr_1.1.1

loaded via a namespace (and not attached): [1] readxl_1.4.1 uuid_1.1-0 backports_1.4.1
[4] systemfonts_1.0.4 NMF_0.26 plyr_1.8.8
[7] repr_1.1.4 BiocParallel_1.32.4 listenv_0.9.0
[10] ggnetwork_0.5.12 gridBase_0.4-7 digest_0.6.31
[13] foreach_1.5.2 yulab.utils_0.0.6 htmltools_0.5.4
[16] viridis_0.6.2 ggalluvial_0.12.5 fansi_1.0.4
[19] magrittr_2.0.3 googlesheets4_1.0.1 cluster_2.1.4
[22] doParallel_1.0.17 tzdb_0.3.0 sna_2.7-1
[25] ComplexHeatmap_2.15.3 globals_0.16.2 graphlayouts_0.8.4
[28] modelr_0.1.10 matrixStats_0.63.0 timechange_0.1.1
[31] colorspace_2.1-0 rvest_1.0.3 rappdirs_0.3.3
[34] ggrepel_0.9.3 haven_2.5.1 textshaping_0.3.6
[37] crayon_1.5.2 jsonlite_1.8.4 iterators_1.0.14
[40] glue_1.6.2 polyclip_1.10-4 registry_0.5-1
[43] gtable_0.3.3 gargle_1.2.1 GetoptLong_1.0.5
[46] car_3.1-2 future.apply_1.10.0 shape_1.4.6
[49] abind_1.4-5 scales_1.2.1 DBI_1.1.3
[52] rngtools_1.5.2 rstatix_0.7.2 Rcpp_1.0.10
[55] viridisLite_0.4.1 clue_0.3-64 gridGraphics_0.5-1
[58] stats4_4.2.2 httr_1.4.4 FNN_1.1.3.2
[61] RColorBrewer_1.1-3 ellipsis_0.3.2 pkgconfig_2.0.3
[64] farver_2.1.1 dbplyr_2.2.1 utf8_1.2.3
[67] here_1.0.1 tidyselect_1.2.0 labeling_0.4.2
[70] rlang_1.1.0 reshape2_1.4.4 cellranger_1.1.0
[73] munsell_0.5.0 tools_4.2.2 cli_3.6.1
[76] generics_0.1.3 statnet.common_4.8.0 broom_1.0.4
[79] evaluate_0.20 fastmap_1.1.0 ragg_1.2.4
[82] fs_1.6.1 tidygraph_1.2.3 pbapply_1.7-0
[85] future_1.32.0 xml2_1.3.3 compiler_4.2.2
[88] png_0.1-8 ggsignif_0.6.4 reprex_2.0.2
[91] tweenr_2.0.2 stringi_1.7.12 RSpectra_0.16-1
[94] lattice_0.20-45 IRdisplay_1.1 Matrix_1.5-3
[97] vctrs_0.6.1 pillar_1.9.0 lifecycle_1.0.3
[100] BiocManager_1.30.20 GlobalOptions_0.1.2 BiocNeighbors_1.16.0 [103] cowplot_1.1.1 irlba_2.3.5.1 R6_2.5.1
[106] network_1.18.1 gridExtra_2.3 IRanges_2.32.0
[109] parallelly_1.35.0 codetools_0.2-18 MASS_7.3-58.1
[112] assertthat_0.2.1 rprojroot_2.0.3 rjson_0.2.21
[115] withr_2.5.0 S4Vectors_0.36.2 hms_1.1.2
[118] parallel_4.2.2 IRkernel_1.3.1 coda_0.19-4
[121] carData_3.0-5 googledrive_2.0.0 ggpubr_0.6.0
[124] pbdZMQ_0.3-8 ggforce_0.4.1 lubridate_1.9.0
[127] base64enc_0.1-3

Thank you for any help you can offer.

pwmellors commented 1 year ago

Try this - with this approach you need to specify a filepath for the pdf (I made one up), make a plot object from the netVisual function and then repeat the plot object name prior to dev.off()

pdf('/users/myname/myfiles/test_plot.pdf') testplot <- netVisual_circle(cellchat@net$count, vertex.weight = groupSize, weight.scale = T, label.edge= F, title.name = "Number of Interactions") testplot dev.off()

mhulke commented 1 year ago

This worked! Thank you for the help!