error when specifying topics for ontologyDotPlot

[danielgchen]

Hi, after computing GREAT I tried using ontologyDotPlot, but I kept on getting an error when trying to specify the topics to plot, below I've attached a screenshot of my cistopic object, specifically the GREAT portion and the different attempts I've made to specify topics

[cbravo93]

Hi @danielgchen !

Can you run this and paste the output?

topics <- c(1,10)
ontology <- 'GO Biological Process'
GOdata <- llply(topics, function(i) cisTopicObject@binarized.rGREAT[[i]][[ontology]])
sapply(GOdata, nrow)

[danielgchen]

[danielgchen]

I tried using both llply and lapply but both didn't seem to work

[cbravo93]

can you load library(plyr)?

[sinkahak]

Hi, I am having a problem concerning oncologyDotPlot function even after installing and loading plyr.
First, I got the same error as described above. Now that I installed and loaded plyr, I get the following error
when trying to run oncologyDotPlot:

Do you have any suggestions, what I could try to fix this? Am I missing someting obvious? Thanks in advance!

SessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /research/users/sinihak/miniconda3/envs/sc-tutorial/lib/R/lib/libRblas.so

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

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

other attached packages:
[1] plyr_1.8.6
[2] densityClust_0.3
[3] doRNG_1.7.1
[4] rngtools_1.5
[5] foreach_1.5.1
[6] scatterplot3d_0.3-41
[7] plotly_4.9.3
[8] ggplot2_3.3.3
[9] fitdistrplus_1.1-1
[10] survival_3.2-7
[11] Seurat_3.2.2
[12] hdf5r_1.3.3
[13] org.Hs.eg.db_3.10.0
[14] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[15] GenomicFeatures_1.38.2
[16] AnnotationDbi_1.48.0
[17] Biobase_2.46.0
[18] ChIPseeker_1.22.1
[19] rGREAT_1.18.0
[20] GenomicRanges_1.38.0
[21] GenomeInfoDb_1.22.1
[22] IRanges_2.20.2
[23] S4Vectors_0.24.4
[24] BiocGenerics_0.32.0
[25] data.table_1.13.6
[26] fastcluster_1.1.25
[27] ComplexHeatmap_2.2.0
[28] Rtsne_0.15
[29] umap_0.2.7.0
[30] Rsubread_2.0.1
[31] cisTopic_0.3.0
[32] MASS_7.3-53

loaded via a namespace (and not attached):
[1] rappdirs_0.3.1 rtracklayer_1.46.0
[3] pbdZMQ_0.3-3.1 R.methodsS3_1.8.1
[5] pkgmaker_0.32.2 tidyr_1.1.2
[7] bit64_4.0.5 irlba_2.3.3
[9] DelayedArray_0.12.3 R.utils_2.10.1
[11] rpart_4.1-15 doParallel_1.0.14
[13] RCurl_1.98-1.2 generics_0.1.0
[15] snow_0.4-3 RhpcBLASctl_0.20-137
[17] cowplot_1.1.0 RSQLite_2.2.1
[19] RANN_2.6.1 europepmc_0.4
[21] future_1.20.1 bit_4.0.4
[23] enrichplot_1.6.1 spatstat.data_1.5-2
[25] xml2_1.3.2 httpuv_1.5.4
[27] SummarizedExperiment_1.16.1 assertthat_0.2.1
[29] viridis_0.5.1 hms_0.5.3
[31] evaluate_0.14 promises_1.1.1
[33] progress_1.2.2 caTools_1.18.0
[35] dbplyr_2.0.0 igraph_1.2.6
[37] DBI_1.1.0 htmlwidgets_1.5.3
[39] feather_0.3.5 rsparse_0.4.0
[41] purrr_0.3.4 ellipsis_0.3.1
[43] RSpectra_0.16-0 dplyr_1.0.2
[45] annotate_1.64.0 deldir_0.2-3
[47] biomaRt_2.42.1 vctrs_0.3.6
[49] Cairo_1.5-10 ROCR_1.0-11
[51] abind_1.4-5 withr_2.3.0
[53] ggforce_0.3.2 triebeard_0.3.0
[55] sctransform_0.3.1 GenomicAlignments_1.22.1
[57] prettyunits_1.1.1 goftest_1.2-2
[59] cluster_2.1.0 DOSE_3.12.0
[61] IRdisplay_0.7.0 lazyeval_0.2.2
[63] crayon_1.3.4 pkgconfig_2.0.3
[65] tweenr_1.0.1 nlme_3.1-148
[67] rlang_0.4.10 globals_0.13.1
[69] lifecycle_0.2.0 miniUI_0.1.1.1
[71] registry_0.5-1 BiocFileCache_1.10.2
[73] doSNOW_1.0.19 rsvd_1.0.3
[75] polyclip_1.10-0 matrixStats_0.57.0
[77] lmtest_0.9-38 graph_1.64.0
[79] Matrix_1.2-18 urltools_1.7.3
[81] IRkernel_1.1.1 boot_1.3-25
[83] zoo_1.8-8 base64enc_0.1-3
[85] ggridges_0.5.2 GlobalOptions_0.1.2
[87] png_0.1-7 viridisLite_0.3.0
[89] rjson_0.2.20 RcisTarget_1.6.0
[91] float_0.2-4 bitops_1.0-6
[93] R.oo_1.24.0 lda_1.4.2
[95] KernSmooth_2.23-18 Biostrings_2.54.0
[97] blob_1.2.1 shape_1.4.5
[99] stringr_1.4.0 qvalue_2.18.0
[101] parallelly_1.21.0 gridGraphics_0.5-0
[103] scales_1.1.1 memoise_1.1.0
[105] GSEABase_1.48.0 magrittr_2.0.1
[107] ica_1.0-2 gplots_3.1.0
[109] zlibbioc_1.32.0 compiler_3.6.1
[111] RColorBrewer_1.1-2 plotrix_3.7-8
[113] clue_0.3-57 Rsamtools_2.2.3
[115] XVector_0.26.0 listenv_0.8.0
[117] patchwork_1.1.0 pbapply_1.4-3
[119] text2vec_0.6 mgcv_1.8-33
[121] tidyselect_1.1.0 stringi_1.5.3
[123] doMC_1.3.5 GOSemSim_2.12.1
[125] askpass_1.1 ggrepel_0.8.2
[127] fastmatch_1.1-0 tools_3.6.1
[129] future.apply_1.6.0 circlize_0.4.11
[131] uuid_0.1-4 AUCell_1.8.0
[133] gridExtra_2.3 farver_2.0.3
[135] ggraph_2.0.4 digest_0.6.27
[137] rvcheck_0.1.8 BiocManager_1.30.10
[139] FNN_1.1.3 shiny_1.5.0
[141] Rcpp_1.0.5 later_1.1.0.1
[143] RcppAnnoy_0.0.18 httr_1.4.2
[145] colorspace_2.0-0 tensor_1.5
[147] XML_3.99-0.3 reticulate_1.18
[149] splines_3.6.1 lgr_0.4.1
[151] uwot_0.1.8 spatstat.utils_1.17-0
[153] graphlayouts_0.7.1 ggplotify_0.0.5
[155] xtable_1.8-4 jsonlite_1.7.2
[157] spatstat_1.64-1 tidygraph_1.2.0
[159] R6_2.5.0 mlapi_0.1.0
[161] pillar_1.4.7 htmltools_0.5.0
[163] mime_0.9 glue_1.4.2
[165] fastmap_1.0.1 BiocParallel_1.20.1
[167] codetools_0.2-18 fgsea_1.12.0
[169] lattice_0.20-41 tibble_3.0.4
[171] curl_4.3 leiden_0.3.5
[173] gtools_3.8.2 GO.db_3.10.0
[175] openssl_1.4.3 repr_1.1.0
[177] munsell_0.5.0 DO.db_2.9
[179] GetoptLong_1.0.4 GenomeInfoDbData_1.2.2
[181] iterators_1.0.13 reshape2_1.4.4
[183] gtable_0.3.0

[cbravo93]

Hi!

For what I see you don't have any GO term enriched in those topics with those thresholds. You can try decreasing the fold_enrichment or increasing sign. I have added some warnings/error messages when this happens to make it clearer. Topics with no GO terms will not be shown in the dotplot (instead of getting the vector error), and if all topics have no terms you will get an error message specifying that.

Let me know if this is a good explanation for your case :)

Cheers!

C

[sinkahak]

Hi @cbravo93 and thanks for the quick response! I tried to decrease the fold_enrichment and to increase sign (a lot), tried numerous different values and the same error still remains. I also ran the function without defining those two arguments but it didn't work either.

[cbravo93]

Hi @sinihak !

That could still happen if your topics are not very good. Just to be sure that this is the reason (and not something technical), could you upload your topics bed files on the GREAT web version: http://great.stanford.edu/public/html/ ?

Cheers!

C

[sinkahak]

I uploaded the topics on GREAT and it was just fine. I also tried to run the 10 X pbmc 5k dataset in my notebook but the same error occured with oncologyDotPlot.