noriakis
commented
7 months ago Dear @yvazirabad,
Thank you very much for using the package, and reporting the issue. As you stated, the error seems to come from magick package. ggkegg uses the magick internally only in the overlay_raw_map() and the first example in the README.md does not use the function. So it might be related to the ggfx::with_outer_glow function. Could you try the following code without with_outer_glow to see if the error remains?
pathway("ko01100") |>
process_line() |>
highlight_module(module("M00021")) |>
highlight_module(module("M00338")) |>
ggraph(x=x, y=y) +
geom_node_point(size=1, aes(color=I(fgcolor),
filter=fgcolor!="none" & type!="line")) +
geom_edge_link0(width=0.1, aes(color=I(fgcolor),
filter=type=="line"& fgcolor!="none")) +
geom_edge_link0(width=2,
aes(color=I(fgcolor),
filter=(M00021 | M00338))) +
geom_node_point(size=2,
aes(color=I(fgcolor),
filter=(M00021 | M00338))) +
geom_node_text(size=2,
aes(x=x, y=y,
label=graphics_name,
filter=name=="path:ko00270"),
repel=TRUE, family="sans", bg.colour="white") +
theme_void()Sincerely, Noriaki Sato
yvazirabad
Hello,
I am excited to use ggkegg. However, I cannot run the first example code block using pathway "ko01100". I get the error "Error: Image must have single frame to write a native raster." This error seems to come from the magick R package.
https://cpp.hotexamples.com/examples/magick/Blob/-/cpp-blob-class-examples.html#0x39145acda6fd2a210063e9946b2a82f0947bc65496a64405d5733254faf68110-168,,183,
Do you have any idea how this error happens?
Here is my sessionInfo() as well. attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] dplyr_1.1.4 ggfx_1.0.1 ggkegg_1.0.2 tidygraph_1.2.3 igraph_1.5.1 XML_3.99-0.15 ggraph_2.1.0
[8] ggplot2_3.4.4
loaded via a namespace (and not attached): [1] tidyselect_1.2.0 viridisLite_0.4.2 farver_2.1.1 blob_1.2.4
[5] filelock_1.0.2 viridis_0.6.4 Biostrings_2.68.1 bitops_1.0-7
[9] fastmap_1.1.1 RCurl_1.98-1.13 BiocFileCache_2.8.0 tweenr_2.0.2
[13] digest_0.6.33 lifecycle_1.0.4 Cairo_1.6-1 KEGGREST_1.40.0
[17] RSQLite_2.3.3 magrittr_2.0.3 compiler_4.3.1 rlang_1.1.2
[21] tools_4.3.1 utf8_1.2.4 data.table_1.14.8 labeling_0.4.3
[25] graphlayouts_1.0.0 bit_4.0.5 curl_5.1.0 withr_2.5.2
[29] purrr_1.0.2 BiocGenerics_0.48.1 grid_4.3.1 polyclip_1.10-6
[33] stats4_4.3.1 fansi_1.0.5 colorspace_2.1-0 scales_1.2.1
[37] MASS_7.3-60 cli_3.6.1 crayon_1.5.2 ragg_1.2.5
[41] generics_0.1.3 rstudioapi_0.15.0 httr_1.4.7 rjson_0.2.21
[45] DBI_1.1.3 cachem_1.0.8 ggforce_0.4.1 stringr_1.5.0
[49] zlibbioc_1.48.0 AnnotationDbi_1.62.2 XVector_0.40.0 vctrs_0.6.4
[53] shadowtext_0.1.2 IRanges_2.36.0 GetoptLong_1.0.5 patchwork_1.1.3
[57] S4Vectors_0.40.1 bit64_4.0.5 ggrepel_0.9.4 systemfonts_1.0.5
[61] magick_2.7.5 tidyr_1.3.0 glue_1.6.2 stringi_1.8.1
[65] gtable_0.3.4 GenomeInfoDb_1.36.1 munsell_0.5.0 tibble_3.2.1
[69] pillar_1.9.0 GenomeInfoDbData_1.2.11 R6_2.5.1 dbplyr_2.3.3
[73] textshaping_0.3.6 Biobase_2.62.0 png_0.1-8 memoise_2.0.1
[77] Rcpp_1.0.11 gridExtra_2.3 org.Hs.eg.db_3.17.0 pkgconfig_2.0.3
[81] GlobalOptions_0.1.2
Respectfully, Ibrahim Vazirabad