Comments (9)
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)
from cistopic.
from cistopic.
I tried using both llply and lapply but both didn't seem to work
from cistopic.
can you load library(plyr)?
from cistopic.
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
from cistopic.
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
from cistopic.
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.
from cistopic.
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
from cistopic.
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.
from cistopic.
Related Issues (20)
- Question about createcisTopicObject HOT 1
- installation issue with ubuntu 20.04 HOT 3
- possibility to use BAM files from bulk ChIP HOT 1
- annotateRegions with own dataset HOT 1
- createcisTopicObject and genomic coordinates incompatibility error HOT 3
- input from fragments.tsv.gz? HOT 1
- Installation issue HOT 2
- Tutorial Dataset files HOT 1
- tSNE Clustering Thresholds HOT 1
- LDA run with Python and LogLikelihhod HOT 1
- How can I run cisTopic in R 4.0 HOT 2
- Ununsed Arguement error in cisTopic/TcisTarget HOT 1
- cisTopicObject <- selectModel(cisTopicObject) Error in .Call("rs_createGD") : C symbol name "rs_createGD" not in load table HOT 1
- Unused argument error while running topicsRcisTarget
- add cisTopic output to Seurat object? HOT 1
- Running Cistopic HOT 1
- Installation error "Failed to install 'unknown package' from Github: ..." HOT 1
- Loading Multiome data
- sha256sum download failed HOT 1
- Error in metadataFeather(path) : Invalid: Not a feather file HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from cistopic.