java.lang.ClassNotFoundException: GraphColoring when I am trying to run doHMRF

[ZengTaox]

Hi，I am trying to run doHMRF in my windows system and an error happend: 'java.lang.ClassNotFoundException: GraphColoring'. I had installed python packages and R packages before in my r-minconda. I donnot know how to deal with it.

[XuanCao-CX]

Hi @ZengTaox,

From you error information, it looks like you lack GraphColoring package on your windows system. You should make sure that this package have been installed in your windows system. Here is the link [(https://javamana.com/2022/01/202201070431400122.html)] for an example that people got the similar error on windows system and you can fellow the steps.

In addition, we update the doHMRF to doHMRF_V2 and it works well for latest released Giotto master brunch v1.1.0. Here are the codes for running doHMRF_v2 and the parameter can be set for your purposes.

hmrf = initHMRF_V2(gobject = your_giotto_object, spatial_network_name="Delaunay_network", use_spatial_genes="binSpect", k=6, zscore="none", nstart=100)

res_binSpect = doHMRF_V2(hmrf, betas=c(0, 5, 25))

your_giotto_object = addHMRF_V2(gobject = your_giotto_object, HMRFoutput = res_binSpect)

Best, Xuan

[yunbokai]

GraphColoring

Hi @ZengTaox,

From you error information, it looks like you lack GraphColoring package on your windows system. You should make sure that this package have been installed in your windows system. Here is the link [(https://javamana.com/2022/01/202201070431400122.html)] for an example that people got the similar error on windows system and you can fellow the steps.

In addition, we update the doHMRF to doHMRF_V2 and it works well for latest released Giotto master brunch v1.1.0. Here are the codes for running doHMRF_v2 and the parameter can be set for your purposes.

hmrf = initHMRF_V2(gobject = your_giotto_object, spatial_network_name="Delaunay_network", use_spatial_genes="binSpect", k=6, zscore="none", nstart=100)

res_binSpect = doHMRF_V2(hmrf, betas=c(0, 5, 25))

your_giotto_object = addHMRF_V2(gobject = your_giotto_object, HMRFoutput = res_binSpect)

Best, Xuan

Hi @ZengTaox,

From you error information, it looks like you lack GraphColoring package on your windows system. You should make sure that this package have been installed in your windows system. Here is the link [(https://javamana.com/2022/01/202201070431400122.html)] for an example that people got the similar error on windows system and you can fellow the steps.

In addition, we update the doHMRF to doHMRF_V2 and it works well for latest released Giotto master brunch v1.1.0. Here are the codes for running doHMRF_v2 and the parameter can be set for your purposes.

hmrf = initHMRF_V2(gobject = your_giotto_object, spatial_network_name="Delaunay_network", use_spatial_genes="binSpect", k=6, zscore="none", nstart=100)

res_binSpect = doHMRF_V2(hmrf, betas=c(0, 5, 25))

your_giotto_object = addHMRF_V2(gobject = your_giotto_object, HMRFoutput = res_binSpect)

Best, Xuan

Hi there, I got error Error in initHMRF_V2(gobject = visium_T91, spatial_network_name = "Delaunay_network", : could not find function "initHMRF_V2" It seems that library(Giotto) is worked. Could you please tell me how to update the new function?

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] reticulate_1.25 GiottoData_0.1.0 Giotto_2.1

loaded via a namespace (and not attached): [1] tidyselect_1.1.2 remotes_2.4.2 purrr_0.3.4
[4] lattice_0.20-45 colorspace_2.0-3 vctrs_0.4.1
[7] generics_0.1.3 usethis_2.1.6 pracma_2.3.8
[10] utf8_1.2.2 smfishHmrf_0.1 rlang_1.0.4
[13] pkgbuild_1.3.1 R.oo_1.24.0 pillar_1.7.0
[16] withr_2.5.0 glue_1.6.2 DBI_1.1.3
[19] R.utils_2.11.0 rappdirs_0.3.3 sessioninfo_1.2.2 [22] lifecycle_1.0.1 munsell_0.5.0 gtable_0.3.0
[25] R.methodsS3_1.8.1 devtools_2.4.3 memoise_2.0.1
[28] callr_3.7.1 fastmap_1.1.0 ps_1.7.1
[31] curl_4.3.2 parallel_4.1.1 fansi_1.0.3
[34] Rcpp_1.0.9 scales_1.2.0 cachem_1.0.6
[37] pkgload_1.3.0 magick_2.7.3 jsonlite_1.8.0
[40] fs_1.5.2 ggplot2_3.3.6 png_0.1-7
[43] processx_3.7.0 dplyr_1.0.9 rbibutils_2.2.10 [46] grid_4.1.1 rprojroot_2.0.3 Rdpack_2.4
[49] here_1.0.1 cli_3.3.0 tools_4.1.1
[52] magrittr_2.0.3 tibble_3.1.7 crayon_1.5.1
[55] pkgconfig_2.0.3 ellipsis_0.3.2 Matrix_1.4-0
[58] data.table_1.14.2 prettyunits_1.1.1 assertthat_0.2.1 [61] rstudioapi_0.13 R6_2.5.1 compiler_4.1.1