Open hrj21 opened 8 months ago
try this
p = ggcyto(gs[[1]], subset = "root", aes("B710-A", "R780-A")) + geom_hex(bins = 100)
p + axis_x_inverse_trans() + axis_y_inverse_trans()
Not sure why it has to be this way, maybe the latest ggplot changes its behavior, anyway, I don't have time to dig into that, hopefully this works for you
Thanks for such a quick response, but that doesn't make a difference on my end. I'll keep on digging. I'm in a managed environment so not all my packages are up to date, I'll try on a personal setup.
I haven't revisited this before now sorry, but I get the same behaviour with:
I appreciate you might not have time to dig into this but posting this here for more information. Thanks Hefin
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 21.3
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
[4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] scales_1.3.0 ggcyto_1.30.2 ncdfFlow_2.48.0 BH_1.84.0-0
[5] flowCore_2.14.1 openCyto_2.14.0 flowWorkspace_4.14.2 ggplot2_3.5.0
loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 lattice_0.22-5 magrittr_2.0.3 grid_4.3.2
[6] RColorBrewer_1.1-3 plyr_1.8.9 graph_1.80.0 gridExtra_2.3 BiocManager_1.30.22
[11] fansi_1.0.6 XML_3.99-0.16.1 Rgraphviz_2.46.0 textshaping_0.3.7 cli_3.6.2
[16] rlang_1.1.3 RProtoBufLib_2.14.0 Biobase_2.62.0 munsell_0.5.0 withr_3.0.0
[21] cytolib_2.14.1 tools_4.3.2 parallel_4.3.2 dplyr_1.1.4 colorspace_2.1-0
[26] BiocGenerics_0.48.1 vctrs_0.6.5 R6_2.5.1 matrixStats_1.2.0 stats4_4.3.2
[31] lifecycle_1.0.4 zlibbioc_1.48.0 S4Vectors_0.40.2 RBGL_1.78.0 ragg_1.2.7
[36] pkgconfig_2.0.3 pillar_1.9.0 hexbin_1.28.3 gtable_0.3.4 Rcpp_1.0.12
[41] data.table_1.15.2 glue_1.7.0 flowClust_3.40.0 systemfonts_1.0.5 tibble_3.2.1
[46] tidyselect_1.2.0 rstudioapi_0.15.0 farver_2.1.1 labeling_0.4.3 compiler_4.3.2
Hello!
I think this is probably my misunderstanding rather than a bug, but while I can successfully define a new transform that can be applied to a gatingSet, I cannot get ggcyto::axis_x_inverse_trans() to invert it (I think the issue is probably with how I have defined the transform rather than anything to do with ggcyto). Below is a reprex
As you can see, the axes still display the transformed values, not the original ones. What is it I've done wrong here?
Many thanks for your help and an excellent ecosystem of packages. Hefin