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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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plotExprHeatmap function fails #359

Closed isimove closed 6 months ago

isimove commented 1 year ago

I am trying to plot marker expression by cluster_id and sample_id with the plotExprHeatmap() function and I get the following error:

plotExprHeatmap(daf, features = "MHCII", by = "both", k = "meta9", scale = "last", col_clust = FALSE, row_anno = FALSE, bars = FALSE) Error in rbind(1 = c(515, 501, 510, 518.5, 496, 527, 484, 487, 512, : number of columns of matrices must match (see arg 2)

I have looked into the error and it seems to be that the rbind() function fails because there are some cluster with no instances for certain samples. Is there a way to fix it?

HelenaLC commented 1 year ago

Could you please post the output of your sessionInfo()?

isimove commented 1 year ago

sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS

Matrix products: default BLAS/LAPACK: /fast/work/users/isimove_m/miniconda/envs/SpectreR/lib/libopenblasp-r0.3.21.so

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

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

other attached packages: [1] diffcyt_1.18.0 BiocManager_1.30.20 CATALYST_1.22.0 testthat_3.1.8 data.table_1.14.8
[6] Seurat_4.3.0.1 SeuratObject_4.1.3 sp_2.0-0 scater_1.26.1 ggplot2_3.4.2
[11] scuttle_1.8.4 flowCore_2.10.0 cowplot_1.1.1 SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 [16] Biobase_2.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.0
[21] BiocGenerics_0.44.0 MatrixGenerics_1.10.0 matrixStats_0.63.0

loaded via a namespace (and not attached): [1] utf8_1.2.3 spatstat.explore_3.2-1 reticulate_1.25 lme4_1.1-33 tidyselect_1.2.0
[6] htmlwidgets_1.6.2 grid_4.2.3 BiocParallel_1.32.6 Rtsne_0.16 munsell_0.5.0
[11] ScaledMatrix_1.6.0 codetools_0.2-19 ica_1.0-3 future_1.32.0 miniUI_0.1.1.1
[16] withr_2.5.0 spatstat.random_3.1-5 colorspace_2.1-0 progressr_0.13.0 rstudioapi_0.14
[21] ROCR_1.0-11 tensor_1.5 ggsignif_0.6.4 listenv_0.9.0 GenomeInfoDbData_1.2.9
[26] polyclip_1.10-4 farver_2.1.1 parallelly_1.35.0 vctrs_0.6.2 generics_0.1.3
[31] TH.data_1.1-2 R6_2.5.1 doParallel_1.0.17 ggbeeswarm_0.7.2 clue_0.3-64
[36] rsvd_1.0.5 locfit_1.5-9.8 pals_1.7 bitops_1.0-7 spatstat.utils_3.0-3
[41] DelayedArray_0.24.0 promises_1.2.0.1 scales_1.2.1 multcomp_1.4-25 beeswarm_0.4.0
[46] gtable_0.3.3 beachmat_2.14.2 globals_0.16.2 goftest_1.2-3 RProtoBufLib_2.10.0
[51] sandwich_3.0-2 rlang_1.1.1 GlobalOptions_0.1.2 splines_4.2.3 rstatix_0.7.2
[56] lazyeval_0.2.2 dichromat_2.0-0.1 spatstat.geom_3.2-4 broom_1.0.4 reshape2_1.4.4
[61] abind_1.4-5 backports_1.4.1 httpuv_1.6.11 tools_4.2.3 ellipsis_0.3.2
[66] RColorBrewer_1.1-3 ggridges_0.5.4 Rcpp_1.0.10 plyr_1.8.8 sparseMatrixStats_1.10.0
[71] zlibbioc_1.44.0 purrr_1.0.1 RCurl_1.98-1.12 FlowSOM_2.6.0 deldir_1.0-9
[76] ggpubr_0.6.0 pbapply_1.7-2 GetoptLong_1.0.5 viridis_0.6.3 zoo_1.8-12
[81] ggrepel_0.9.3 cluster_2.1.4 colorRamps_2.3.1 magrittr_2.0.3 scattermore_1.2
[86] circlize_0.4.15 lmtest_0.9-40 RANN_2.6.1 mvtnorm_1.1-3 ggnewscale_0.4.8
[91] fitdistrplus_1.1-11 pkgload_1.3.2 patchwork_1.1.2 mime_0.12 xtable_1.8-4
[96] XML_3.99-0.14 gridExtra_2.3 shape_1.4.6 compiler_4.2.3 maps_3.4.0
[101] tibble_3.2.1 KernSmooth_2.23-21 crayon_1.5.2 minqa_1.2.5 htmltools_0.5.5
[106] later_1.3.1 tidyr_1.3.0 tweenr_2.0.2 ComplexHeatmap_2.14.0 MASS_7.3-60
[111] boot_1.3-28.1 Matrix_1.5-4.1 car_3.1-2 brio_1.1.3 cli_3.6.1
[116] parallel_4.2.3 igraph_1.4.3 Spectre_1.0.0 pkgconfig_2.0.3 spatstat.sparse_3.0-2
[121] plotly_4.10.2 foreach_1.5.2 vipor_0.4.5 XVector_0.38.0 drc_3.0-1
[126] stringr_1.5.0 digest_0.6.31 sctransform_0.3.5 RcppAnnoy_0.0.21 ConsensusClusterPlus_1.62.0 [131] spatstat.data_3.0-1 leiden_0.4.3 edgeR_3.40.2 uwot_0.1.16 DelayedMatrixStats_1.20.0
[136] shiny_1.7.4 gtools_3.9.2.1 nloptr_2.0.3 rjson_0.2.21 nlme_3.1-162
[141] lifecycle_1.0.3 jsonlite_1.8.4 carData_3.0-5 BiocNeighbors_1.16.0 mapproj_1.2.8
[146] limma_3.54.2 viridisLite_0.4.2 fansi_1.0.4 pillar_1.9.0 lattice_0.21-8
[151] fastmap_1.1.1 httr_1.4.6 plotrix_3.8-2 survival_3.5-5 remotes_2.4.2
[156] glue_1.6.2 png_0.1-8 iterators_1.0.14 ggforce_0.4.1 stringi_1.7.12
[161] nnls_1.4 BiocSingular_1.14.0 dplyr_1.1.2 cytolib_2.10.0 irlba_2.3.5
[166] future.apply_1.11.0

HelenaLC commented 8 months ago

sorry for the lack of response, but it's hard to help when there's little info or a way of reproducing/understanding the issue... it this issue still persisting, or can it be closed?

HelenaLC commented 6 months ago

closing due to inactivity - also, noting that the current release version is 1.26 (session info above states 1.22, though it's not clear whether or not the issue may still persist)