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Showing content from https://github.com/stuart-lab/signac/issues/522 below:

Using group.by in PlotFootprint results in "Error: Must request at least one colour from a hue palette." · Issue #522 · stuart-lab/signac · GitHub

Hi there,

I've been having an issue with using the PlotFootprint function. Any time I use the group.by argument I end up getting the error "Error: Must request at least one colour from a hue palette." I can plot the variables I have been trying to use for this just fine if I set them as the active identity first, just not using group.by .
I have noticed too that if I assign the plot to a variable, normally it gets saved as a "Large Patchwork (10 elements, 1.3MB)", which is what I would expect, but the same plot using group.by just gets saved as a "List of 10"

So as an example,

PlotFootprint(combined, features = "SIX2", group.by = "predicted.id")

just gives the error. But

Idents(combined) <- "predicted.id"
PlotFootprint(combined, features = "SIX2")

gives the plot I would have expected from the first command.

I don't know if its a bug or if I'm doing something wrong, so any help would be appreciated.

Thanks!

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

attached base packages:
[1] grid splines parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] motifmatchr_1.12.0 TFBSTools_1.28.0 JASPAR2020_0.99.10 SeuratWrappers_0.3.0 cicero_1.8.1
[6] Gviz_1.34.1 monocle_2.18.0 DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-5
[11] Matrix_1.3-2 patchwork_1.1.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.5
[16] purrr_0.3.4 readr_1.4.0 tidyr_1.1.3 tibble_3.1.0 tidyverse_1.3.0
[21] ggplot2_3.3.3 BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.58.0 rtracklayer_1.50.0 Biostrings_2.58.0
[26] XVector_0.30.0 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.14.0 AnnotationFilter_1.14.0 GenomicFeatures_1.42.2
[31] AnnotationDbi_1.52.0 Biobase_2.50.0 future_1.21.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.4
[36] IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.0 SeuratObject_4.0.0 Seurat_4.0.1
[41] Signac_1.1.1

loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SnowballC_0.7.0 scattermore_0.7 GGally_2.1.1 R.methodsS3_1.8.1 bit64_4.0.5
[7] knitr_1.31 R.utils_2.10.1 DelayedArray_0.16.2 data.table_1.14.0 rpart_4.1-15 KEGGREST_1.30.1
[13] RCurl_1.98-1.3 generics_0.1.0 cowplot_1.1.1 RSQLite_2.2.4 RANN_2.6.1 combinat_0.0-8
[19] bit_4.0.4 spatstat.data_2.0-0 xml2_1.3.2 lubridate_1.7.10 httpuv_1.5.5 SummarizedExperiment_1.20.0
[25] assertthat_0.2.1 DirichletMultinomial_1.32.0 viridis_0.5.1 xfun_0.22 hms_1.0.0 promises_1.2.0.1
[31] fansi_0.4.2 progress_1.2.2 caTools_1.18.1 dbplyr_2.1.0 readxl_1.3.1 igraph_1.2.6
[37] DBI_1.1.1 htmlwidgets_1.5.3 sparsesvd_0.2 reshape_0.8.8 spatstat.geom_1.65-5 ellipsis_0.3.1
[43] backports_1.2.1 annotate_1.68.0 biomaRt_2.46.3 deldir_0.2-10 MatrixGenerics_1.2.1 vctrs_0.3.6
[49] remotes_2.2.0 ROCR_1.0-11 abind_1.4-5 cachem_1.0.4 withr_2.4.1 ggforce_0.3.3
[55] checkmate_2.0.0 sctransform_0.3.2 GenomicAlignments_1.26.0 prettyunits_1.1.1 goftest_1.2-2 cluster_2.1.1
[61] seqLogo_1.56.0 lazyeval_0.2.2 crayon_1.4.1 labeling_0.4.2 pkgconfig_2.0.3 slam_0.1-48
[67] tweenr_1.0.1 nlme_3.1-152 ProtGenerics_1.22.0 nnet_7.3-15 rlang_0.4.10 globals_0.14.0
[73] lifecycle_1.0.0 miniUI_0.1.1.1 BiocFileCache_1.14.0 rsvd_1.0.3 modelr_0.1.8 dichromat_2.0-0
[79] cellranger_1.1.0 polyclip_1.10-0 matrixStats_0.58.0 lmtest_0.9-38 graph_1.68.0 ggseqlogo_0.1
[85] zoo_1.8-9 reprex_1.0.0 base64enc_0.1-3 ggridges_0.5.3 pheatmap_1.0.12 png_0.1-7
[91] viridisLite_0.3.0 bitops_1.0-6 R.oo_1.24.0 KernSmooth_2.23-18 blob_1.2.1 parallelly_1.24.0
[97] jpeg_0.1-8.1 CNEr_1.26.0 scales_1.1.1 memoise_2.0.0 magrittr_2.0.1 plyr_1.8.6
[103] ica_1.0-2 zlibbioc_1.36.0 compiler_4.0.4 HSMMSingleCell_1.10.0 RColorBrewer_1.1-2 fitdistrplus_1.1-3
[109] Rsamtools_2.6.0 cli_2.3.1 listenv_0.8.0 pbapply_1.4-3 htmlTable_2.1.0 Formula_1.2-4
[115] MASS_7.3-53.1 mgcv_1.8-33 tidyselect_1.1.0 stringi_1.5.3 densityClust_0.3 askpass_1.1
[121] latticeExtra_0.6-29 ggrepel_0.9.1 VariantAnnotation_1.36.0 fastmatch_1.1-0 tools_4.0.4 future.apply_1.7.0
[127] rstudioapi_0.13 TFMPvalue_0.0.8 foreign_0.8-81 lsa_0.73.2 gridExtra_2.3 farver_2.1.0
[133] Rtsne_0.15 digest_0.6.27 BiocManager_1.30.10 pracma_2.3.3 FNN_1.1.3 shiny_1.6.0
[139] qlcMatrix_0.9.7 Rcpp_1.0.6 broom_0.7.5 later_1.1.0.1 RcppAnnoy_0.0.18 OrganismDbi_1.32.0
[145] httr_1.4.2 ggbio_1.38.0 biovizBase_1.38.0 colorspace_2.0-0 rvest_1.0.0 XML_3.99-0.6
[151] fs_1.5.0 tensor_1.5 reticulate_1.18 uwot_0.1.10 RBGL_1.66.0 RcppRoll_0.3.0
[157] spatstat.utils_2.1-0 plotly_4.9.3 xtable_1.8-4 poweRlaw_0.70.6 jsonlite_1.7.2 R6_2.5.0
[163] Hmisc_4.5-0 pillar_1.5.1 htmltools_0.5.1.1 mime_0.10 glue_1.4.2 fastmap_1.1.0
[169] BiocParallel_1.24.1 codetools_0.2-18 utf8_1.2.1 lattice_0.20-41 spatstat.sparse_2.0-0 curl_4.3
[175] leiden_0.3.7 gtools_3.8.2 GO.db_3.12.1 openssl_1.4.3 limma_3.46.0 survival_3.2-7
[181] docopt_0.7.1 fastICA_1.2-2 munsell_0.5.0 GenomeInfoDbData_1.2.4 haven_2.3.1 reshape2_1.4.4
[187] gtable_0.3.0 spatstat.core_1.65-5

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