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rezakj / iCellR

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
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Can not run findMarkers #15

Closed Yale73 closed 4 years ago

Yale73 commented 4 years ago

Hi iCellR team,

Thanks for developing such a great package. The plots look really cool. Recently, I am using the iCellR to make some plots, but I got error when I ran the findMarkers. It's a long description, thanks for your patience.

I made the object from the seurat object, which includes 21 samples. I choose the integrated data to transfer them. The code is here:

transfer data from seurat object

my.data <- as.data.frame(as.matrix(Seurat_object@assays[["integrated"]]@data))

Create iCellR object

my.obj <- make.obj(my.data)

make sure it's made properly

slotNames(my.obj) my.obj

add seurat parameter

add main data

my.obj@main.data <- as.data.frame(as.matrix(Seurat_object@assays[["integrated"]]@data))

add scaled data

my.obj@scaled.data <- as.data.frame(as.matrix(Seurat_object@assays[["integrated"]]@scale.data))

add cluster

Idents(Seurat_object) <- Seurat_object$seurat_clusters Clust <- as.data.frame(as.matrix(Seurat_object@active.ident)) colnames(Clust) <- "clusters" my.obj@best.clust <- Clust

add conditon1

Idents(Seurat_object) <- Seurat_object$treat treat <- as.data.frame(as.matrix(Seurat_object@active.ident)) colnames(treat) <- "treat" my.obj@extra.data1 <- treat

add conditon2

Idents(Seurat_object) <- Seurat_object$cond Cond <- as.data.frame(as.matrix(Seurat_object@active.ident)) colnames(Cond) <- "Cond" my.obj@extra.data2 <- Cond

add dim reductions

my.obj@tsne.data <- as.data.frame(as.matrix(Seurat_object@reductions[["tsne"]]@cell.embeddings)) my.obj@umap.data <- as.data.frame(as.matrix(Seurat_object@reductions[["umap"]]@cell.embeddings)) my.obj@pca.data <- as.data.frame(as.matrix(Seurat_object@reductions[["pca"]]@cell.embeddings))

All these steps are no error, but when I run findMarkers, I got the following error again and again.

Finding markers for cluster: 1 ... Finding markers for cluster: 2 ... Finding markers for cluster: 3 ... Finding markers for cluster: 4 ... Finding markers for cluster: 5 ... Finding markers for cluster: 6 ... Finding markers for cluster: 7 ... Finding markers for cluster: 8 ... Finding markers for cluster: 9 ... Finding markers for cluster: 10 ... Finding markers for cluster: 11 ... Finding markers for cluster: 12 ... Finding markers for cluster: 13 ... Finding markers for cluster: 14 ... Finding markers for cluster: 15 ... Finding markers for cluster: 16 ... Finding markers for cluster: 17 ... Finding markers for cluster: 18 ... Finding markers for cluster: 19 ... Finding markers for cluster: 20 ... Finding markers for cluster: 21 ... Finding markers for cluster: 22 ... Finding markers for cluster: 23 ... Error in t.test.default(x = mrgd[Cond1_Start:Cond1_End], y = mrgd[Cond2_Start:Cond2_End]) : not enough 'x' observations In addition: There were 22 warnings (use warnings() to see them)

At first, I thought it was the MyClusts, as after we run the following code, the cluster numbers changed to 1, 2, 3,.... from 0, 1, 2, ....

MyClusts <- as.numeric(unique(DATA$clusters)) MyClusts <- sort(MyClusts)

Then I added one step before MyClusts <- sort(MyClusts)

MyClusts <- MyClusts-1

But I still got the same error.

I also extracted the loop part and only run 1 cluster, and I got the following error:

Finding markers for cluster: 1 ... Error in dat : object 'dat' not found

My sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] iCellR_1.4.5 plotly_4.9.2.1 gridExtra_2.3 gtable_0.3.0 RColorBrewer_1.1-2 [6] pheatmap_1.0.12 forcats_0.5.0 stringr_1.4.0 purrr_0.3.3 readr_1.3.1
[11] tidyr_1.0.2 tibble_3.0.0 tidyverse_1.3.0 pryr_0.1.4 magrittr_1.5
[16] data.table_1.12.8 cowplot_1.0.0 Matrix_1.2-18 dplyr_0.8.5 formattable_0.2.0.1 [21] classInt_0.4-3 xlsx_0.6.3 clustree_0.4.2 ggraph_2.0.2 ggplot2_3.3.0
[26] Seurat_3.1.4

loaded via a namespace (and not attached): [1] reticulate_1.14 tidyselect_1.0.0 htmlwidgets_1.5.1 Rtsne_0.15 munsell_0.5.0
[6] codetools_0.2-16 mutoss_0.1-12 ica_1.0-2 future_1.17.0 withr_2.2.0
[11] colorspace_1.4-1 Biobase_2.46.0 knitr_1.28 rstudioapi_0.11 stats4_3.6.2
[16] ROCR_1.0-7 ggsignif_0.6.0 rJava_0.9-11 gbRd_0.4-11 listenv_0.8.0
[21] Rdpack_0.11-1 mnormt_1.5-6 polyclip_1.10-0 bit64_0.9-7 farver_2.0.3
[26] vctrs_0.2.4 generics_0.0.2 TH.data_1.0-10 xfun_0.13 R6_2.4.1
[31] graphlayouts_0.6.0 rsvd_1.0.3 hdf5r_1.3.2 reshape_0.8.8 bitops_1.0-6
[36] assertthat_0.2.1 promises_1.1.0 scales_1.1.0 nnet_7.3-12 multcomp_1.4-13
[41] npsurv_0.4-0 globals_0.12.5 tidygraph_1.1.2 sandwich_2.5-1 rlang_0.4.5
[46] scatterplot3d_0.3-41 splines_3.6.2 lazyeval_0.2.2 acepack_1.4.1 checkmate_2.0.0
[51] broom_0.5.6 reshape2_1.4.3 modelr_0.1.6 backports_1.1.6 httpuv_1.5.2
[56] Hmisc_4.4-0 tools_3.6.2 ellipsis_0.3.0 gplots_3.0.3 ggdendro_0.1-20
[61] BiocGenerics_0.32.0 ggridges_0.5.2 TFisher_0.2.0 Rcpp_1.0.4.6 plyr_1.8.6
[66] base64enc_0.1-3 progress_1.2.2 prettyunits_1.1.1 ggpubr_0.2.5 rpart_4.1-15
[71] pbapply_1.4-2 viridis_0.5.1 zoo_1.8-7 haven_2.2.0 ggrepel_0.8.2
[76] cluster_2.1.0 fs_1.4.1 NbClust_3.0 lmtest_0.9-37 reprex_0.3.0
[81] RANN_2.6.1 mvtnorm_1.1-0 fitdistrplus_1.0-14 hms_0.5.3 xlsxjars_0.6.1
[86] patchwork_1.0.0.9000 lsei_1.2-0 mime_0.9 evaluate_0.14 xtable_1.8-4
[91] jpeg_0.1-8.1 readxl_1.3.1 compiler_3.6.2 KernSmooth_2.23-16 crayon_1.3.4
[96] htmltools_0.4.0 later_1.0.0 Formula_1.2-3 lubridate_1.7.8 DBI_1.1.0
[101] tweenr_1.0.1 dbplyr_1.4.3 MASS_7.3-51.4 rappdirs_0.3.1 cli_2.0.2
[106] gdata_2.18.0 parallel_3.6.2 metap_1.3 igraph_1.2.4.2 pkgconfig_2.0.3
[111] sn_1.6-1 foreign_0.8-72 numDeriv_2016.8-1.1 xml2_1.3.0 multtest_2.42.0
[116] bibtex_0.4.2.2 rvest_0.3.5 digest_0.6.25 sctransform_0.2.1 RcppAnnoy_0.0.16
[121] tsne_0.1-3 rmarkdown_2.1 cellranger_1.1.0 leiden_0.3.3 htmlTable_1.13.3
[126] uwot_0.1.8 shiny_1.4.0.2 gtools_3.8.1 lifecycle_0.2.0 nlme_3.1-142
[131] jsonlite_1.6.1 viridisLite_0.3.0 fansi_0.4.1 pillar_1.4.3 lattice_0.20-38
[136] fastmap_1.0.1 httr_1.4.1 plotrix_3.7-8 survival_3.1-8 glue_1.4.0
[141] png_0.1-7 bit_1.1-15.2 ggforce_0.3.1 class_7.3-15 stringi_1.4.6
[146] latticeExtra_0.6-29 caTools_1.18.0 irlba_2.3.3 e1071_1.7-3 future.apply_1.5.0
[151] ape_5.3

Thanks for your help.

Best, Yale

rezakj commented 4 years ago

It seems like one of your clusters has less than 2 cells? How many cells are in each cluster?

Reza

Yale73 commented 4 years ago

Hi Reza,

There are a lot cells. Here are the cluster numbers.

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
21631 17052 11645 9271 7892 7861 7390 6922 6479 3610 3604 2354 1897 1779 1603 961 920 904 533 490 339 292 253

Thanks, Yale

rezakj commented 4 years ago

Can you print my.obj.

Yale73 commented 4 years ago

The print results:

################################### ,--. ,-----. ,--.,--.,------. --'' .--./ ,---. | || || .--. ' ,--.| | | .-. :| || || '--'.' | |' '--'\ --. | || || | --' -----'----'--'--'`--' '--' ################################### An object of class iCellR version: 1.4.5 Raw/original data dimentions (rows,columns): 4000,115682 Data conditions in raw data: AAACCCAAGAAGTCTA,AAACCCAAGAATCGCG,AAACCCAAGAATCTAG,AAACCCAAGACACACG,AAACCCAAGACCGCCT,AAACCCAAGAGAGAAC,AAACCCAAGAGTCAGC,AAACCCAAGAGTTCGG,AAACCCAAGATGTTCC,AAACCCAAGCACGGAT,AAACCCAAGCAGGCTA,AAACCCAAGCATGTTC,AAACCCAAGCATTGAA-1,AAACCCAAGCGCTGCT,AAACCCAAGCGTATAA,AAACCCAAGCGTTCAT,AAACCCAAGCTTTGTG,AAACCCAAGGACGGAG,AAACCCAAGGATGTTA,AAACCCAAGGCAGTCA,AAACCCAAGGCTGGAT,AAACCCAAGGGACACT,AAACCCAAGGGCAGTT,AAACCCAAGGTCGTCC,AAACCCAAGGTCTTTG,AAACCCAAGGTTAAAC-1,AAACCCAAGTATGATG,AAACCCAAGTCATAGA,AAACCCAAGTCCGCGT,AAACCCAAGTCGGCAA,AAACCCAAGTGCTCGC,AAACCCAAGTGGCGAT,AAACCCAAGTTCCTGA-1,AAACCCACAACCAATC,AAACCCACAACGATTC,AAACCCACAAGTGATA,AAACCCACAAGTGGGT,AAACCCACAATACAGA,AAACCCACACGAAGAC,AAACCCACACTGCTTC,AAACCCACACTGGCCA,AAACCCACACTTGAAC,AAACCCACAGAAATCA,AAACCCACAGAGGGTT-1,AAACCCACAGAGGTAC,AAACCCACAGAGTCTT,AAACCCACAGATAAAC,AAACCCACAGCAGAAC,AAACCCACAGCGAGTA,AAACCCACAGGACTTT,AAACCCACAGGCTTGC,AAACCCACAGGTGGAT,AAACCCACAGTCCGTG,AAACCCACAGTTCTAG-1,AAACCCACATAACGGG,AAACCCACATCAGCTA,AAACCCACATCGATAC,AAACCCACATCGATCA,AAACCCACATCTGGGC,AAACCCACATGACTGT,AAACCCACATGTCTAG,AAACCCACATTAGGCT,AAACCCACATTGTACG,AAACCCAGTAACATAG,AAACCCAGTAACGTTC,AAACCCAGTAAGGTCG,AAACCCAGTACTGAGG-1,AAACCCAGTACTGTTG,AAACCCAGTACTTCCC-1,AAACCCAGTAGCCAGA,AAACCCAGTATTTCTC-1,AAACCCAGTCACCGCA,AAACCCAGTCACTCGG,AAACCCAGTCCGGACT,AAACCCAGTCGGTGTC,AAACCCAGTCGTACAT,AAACCCAGTCGTTTCC,AAACCCAGTCTCAGAT,AAACCCAGTGAGACGT,AAACCCAGTGAGTGAC,AAACCCAGTGGTATGG,AAACCCAGTGTAGGAC,AAACCCAGTGTATTCG,AAACCCAGTGTCATCA,AAACCCAGTGTGAATA,AAACCCAGTTAGAAGT,AAACCCAGTTAGGCCC,AAACCCAGTTTAAGGA,AAACCCAGTTTCACAG,AAACCCATCACACCCT,AAACCCATCACCATGA,AAACCCATCACTACTT,AAACCCATCACTAGCA,AAACCCATCAGAGTTC,AAACCCATCATGCATG-1,AAACCCATCCATGCAA,AAACCCATCCATTTCA,AAACCCATCCCAATAG,AAACCCATCCCTGGTT,AAACCCATCCGCACGA,AAACCCATCCGGTAGC,AAACCCATCCGTGTAA,AAACCCATCCTACAAG,AAACCCATCCTACGAA,AAACCCATCCTGCCAT,AAACCCATCCTGTTAT,AAACCCATCCTTATGT,AAACCCATCGAGATAA,AAACCCATCGAGTACT,AAACCCATCGCCAATA,AAACCCATCGGCCCAA,AAACCCATCGGTAGAG-1,AAACCCATCGGTCATA,AAACCCATCGTAGCTA,AAACCCATCTAAGCCA,AAACCCATCTCACCCA,AAACCCATCTCCTGTG,AAACCCATCTGCTGAA,AAACCCATCTGTGCTC,AAACCCATCTTAGCAG,AAACCCATCTTAGTTC,AAACCCATCTTCCCAG,AAACCCATCTTCTCAA,AAACCCATCTTTCCGG,AAACGAAAGACGGATC,AAACGAAAGAGAACCC,AAACGAAAGAGGACTC,AAACGAAAGAGTCACG,AAACGAAAGATCACTC,AAACGAAAGATCCGAG,AAACGAAAGATTTGCC,AAACGAAAGCAGGCTA,AAACGAAAGCATGCGA,AAACGAAAGCCTGAGA,AAACGAAAGCGACCCT,AAACGAAAGCTGACCC,AAACGAAAGCTGACTT,AAACGAAAGCTGAGTG,AAACGAAAGCTTCTAG,AAACGAAAGGACCCAA,AAACGAAAGGACTGGT,AAACGAAAGGCTTCCG,AAACGAAAGGGATCAC,AAACGAAAGGGCATGT,AAACGAAAGGGCCAAT,AAACGAAAGGGTACGT,AAACGAAAGGGTTAGC,AAACGAAAGGTACCTT,AAACGAAAGGTGCTTT,AAACGAAAGGTTGGAC,AAACGAAAGTATTCCG,AAACGAAAGTCTCCTC,AAACGAAAGTGAGTTA,AAACGAAAGTTACGTC,AAACGAAAGTTGGCGA,AAACGAAAGTTGGCTT,AAACGAACAAACTGCT,AAACGAACAAAGGGTC,AAACGAACAAAGGTTA,AAACGAACAAATTGGA,AAACGAACAACACAAA,AAACGAACAACGCCCA-1,AAACGAACAACTCGAT,AAACGAACAATAGTAG,AAACGAACAATCACGT,AAACGAACACACCGCA,AAACGAACACACCTAA,AAACGAACACCATATG,AAACGAACACCATTCC,AAACGAACACCGTGGT,AAACGAACACGCGCTA,AAACGAACACGGTGTC,AAACGAACACTGTCGG,AAACGAACAGAACCGA,AAACGAACAGAGGGTT,AAACGAACAGATCACT,AAACGAACAGCCTTCT,AAACGAACAGGATGAC-1,AAACGAACAGTTGTTG,AAACGAACATACCAGT,AAACGAACATATCTGG,AAACGAACATCATCCC,AAACGAACATCATTTC,AAACGAACATCCGAGC,AAACGAACATCGCTAA-1,AAACGAACATGAATCC,AAACGAACATGACGAG,AAACGAACATGCAGCC,AAACGAACATGCTGCG,AAACGAACATGTGCCG,AAACGAACATTGACCA,AAACGAAGTACAAAGT,AAACGAAGTACCGCGT,AAACGAAGTACCGGAA,AAACGAAGTAGAAACT,AAACGAAGTAGAATGT,AAACGAAGTAGACGGT,AAACGAAGTAGTCGTT,AAACGAAGTATCAAGA,AAACGAAGTCACTTAG,AAACGAAGTCCCACGA,AAACGAAGTCGTAATC,AAACGAAGTCTACATG-1,AAACGAAGTCTACTGA,AAACGAAGTCTATGAC,AAACGAAGTCTGCAAT,AAACGAAGTCTGCCTT,AAACGAAGTCTGTCAA,AAACGAAGTCTTGTCC,AAACGAAGTGCACATT,AAACGAAGTGCATCTA,AAACGAAGTGCCCAGT-1,AAACGAAGTGCGTTTA,AAACGAAGTGGGTCAA,AAACGAAGTTGAGGAC,AAACGAAGTTGTGTAC,AAACGAAGTTTACCTT,AAACGAATCAACCCGG,AAACGAATCAACTGAC,AAACGAATCAATGTCG,AAACGAATCACTCACC,AAACGAATCAGCACCG,AAACGAATCAGCTCTC,AAACGAATCAGGTGTT,AAACGAATCATGAAAG,AAACGAATCCACACAA,AAACGAATCCATTGGA,AAACGAATCCTGATAG,AAACGAATCGAACCTA,AAACGAATCGAATCCA,AAACGAATCGAGGCAA,AAACGAATCGCGGACT,AAACGAATCGCGTAGC,AAACGAATCGCTAAAC,AAACGAATCGCTTTAT,AAACGAATCGGACAAG,AAACGAATCGGTATGT,AAACGAATCGTCAAAC,AAACGAATCGTTATCT,AAACGAATCTACTTCA,AAACGAATCTCGACCT,AAACGAATCTGGTGGC,AAACGAATCTTCCAGC,AAACGAATCTTTACAC,AAACGCTAGAATACAC,AAACGCTAGAATCGCG,AAACGCTAGACCGCCT-1,AAACGCTAGAGATTCA,AAACGCTAGAGCAAGA,AAACGCTAGAGCAGAA,AAACGCTAGATAACAC,AAACGCTAGATGACAT,AAACGCTAGATGGCGT,AAACGCTAGCAACCAG,AAACGCTAGCCAGACA,AAACGCTAGCCATATC,AAACGCTAGCCATTTG,AAACGCTAGGAACTAT,AAACGCTAGGACAACC,AAACGCTAGGATTCAA,AAACGCTAGGCACCAA,AAACGCTAGGCAGGGA,AAACGCTAGGCCGCTT,AAACGCTAGGCTCAAG,AAACGCTAGGGCGAAG,AAACGCTAGGTAGCCA,AAACGCTAGGTCTGGA,AAACGCTAGGTTACAA,AAACGCTAGTAAGCAT,AAACGCTAGTACTGTC-1,AAACGCTAGTATGATG,AAACGCTAGTCGAAGC,AAACGCTAGTGCTACT-1,AAACGCTAGTGGCAGT,AAACGCTAGTTCCATG,AAACGCTAGTTGCATC-1,AAACGCTAGTTGTAGA,AAACGCTCAAACGGCA,AAACGCTCAAAGGCGT,AAACGCTCAAATCAGA-1,AAACGCTCAACGACAG,AAACGCTCAACTGATC,AAACGCTCAAGCAATA,AAACGCTCAAGTGGCA,AAACGCTCAATCTCTT,AAACGCTCAATGAACA,AAACGCTCAATTCTTC,AAACGCTCACACCAGC,AAACGCTCACCGTGAC,AAACGCTCACGGCACT,AAACGCTCACTACCGG-1,AAACGCTCACTATCGA,AAACGCTCACTCCGAG,AAACGCTCACTGGCGT,AAACGCTCACTTACAG,AAACGCTCACTTGAAC,AAACGCTCAGAGAAAG,AAACGCTCAGAGGACT-1,AAACGCTCAGAGTCTT,AAACGCTCAGATGCGA,AAACGCTCAGCCCAGT,AAACGCTCAGCGTACC,AAACGCTCAGGCACTC,AAACGCTCAGGGCTTC,AAACGCTCAGTAACCT,AAACGCTCATAACTCG,AAACGCTCATACTGAC,AAACGCTCATAGGCGA,AAACGCTCATCCTTCG,AAACGCTCATCTAGAC,AAACGCTCATGGCCAC,AAACGCTCATTGGGAG,AAACGCTGTACGTAGG,AAACGCTGTACTCAAC,AAACGCTGTAGAATGT,AAACGCTGTAGACAAT,AAACGCTGTAGTACGG,AAACGCTGTCCTTGTC,AAACGCTGTCGAGTTT,AAACGCTGTGATTAGA,AAACGCTGTGCAGATG,AAACGCTGTGCCGAAA,AAACGCTGTGCGCTCA,AAACGCTGTGGATACG,AAACGCTGTGGATGAC-1,AAACGCTGTGTCATGT,AAACGCTGTGTCGCTG,AAACGCTGTGTGCTTA,AAACGCTGTTAAGACA,AAACGCTGTTACGATC,AAACGCTGTTAGGCTT,AAACGCTGTTCAAGGG,AAACGCTGTTCCCACT,AAACGCTGTTCGGACC,AAACGCTGTTTACGAC,AAACGCTTCAAGTCGT,AAACGCTTCAATCAGC,AAACGCTTCAATCCAG,AAACGCTTCAATCTCT,AAACGCTTCACGAACT,AAACGCTTCACTAGCA,AAACGCTTCAGGTGTT,AAACGCTTCAGTAGGG,AAACGCTTCATAGACC,AAACGCTTCATCGCTC,AAACGCTTCATCTATC,AAACGCTTCATGAGGG-1,AAACGCTTCATGGGAG,AAACGCTTCCACATAG,AAACGCTTCCACGAAT,AAACGCTTCCATCCGT,AAACGCTTCCATTGTT,AAACGCTTCCGAGAAG,AAACGCTTCCGAGTGC,AAACGCTTCCGGCAAC,AAACGCTTCCGTCAAA,AAACGCTTCCTCATAT,AAACGCTTCGACCACG,AAACGCTTCGACGACC-1,AAACGCTTCGCTTAAG,AAACGCTTCGGCTGAC,AAACGCTTCGGTGCAC,AAACGCTTCGTTCTCG,AAACGCTTCTACAGGT,AAACGCTTCTACGGGC,AAACGCTTCTATGCCC,AAACGCTTCTATTCGT,AAACGCTTCTCCGATC,AAACGCTTCTCGAACA,AAACGCTTCTCGCTCA,AAACGCTTCTCTCTTC,AAACGCTTCTGTGCAA,AAACGCTTCTTACCGC,AAACGCTTCTTAGGAC,AAACGCTTCTTTCAGT,AAAGAACAGAAGCTCG,AAAGAACAGACCAAAT,AAAGAACAGAGCATAT,AAAGAACAGATCCCGC,AAAGAACAGCCGAACA,AAAGAACAGCCGAATG,AAAGAACAGCGCCTCA,AAAGAACAGGACAGCT,AAAGAACAGGATTTAG,AAAGAACAGGATTTCC,AAAGAACAGGGTTGCA,AAAGAACAGGTATCTC,AAAGAACAGTAACGTA,AAAGAACAGTACAACA,AAAGAACAGTCCCAAT,AAAGAACAGTCGTCTA,AAAGAACAGTCTTCGA,AAAGAACAGTTGAAGT-1,AAAGAACCAAAGTGTA,AAAGAACCAAGCCCAC,AAAGAACCAATCAGCT,AAAGAACCAATCTCGA,AAAGAACCAATCTGCA,AAAGAACCACAGTATC,AAAGAACCACCCGTAG,AAAGAACCACCCTAAA,AAAGAACCACGCCAGT,AAAGAACCAGAAATTG,AAAGAACCAGACAAGC,AAAGAACCAGACCAGA-1,AAAGAACCAGACCTGC,AAAGAACCAGCAGTCC,AAAGAACCAGCCTATA,AAAGAACCAGGCTATT,AAAGAACCAGTAGTTC,AAAGAACCATCTATCT,AAAGAACCATGAGAAT,AAAGAACCATGCAGGA,AAAGAACCATTGACTG,AAAGAACGTAACGATA-1,AAAGAACGTACAAGCG,AAAGAACGTACCCGAC,AAAGAACGTACCCGCA,AAAGAACGTACGTAGG,AAAGAACGTACTCCCT,AAAGAACGTACTCGTA,AAAGAACGTAGGCAAC,AAAGAACGTAGGTTTC,AAAGAACGTAGTCTGT,AAAGAACGTATGACAA,AAAGAACGTCAGTTTG,AAAGAACGTCATAAAG,AAAGAACGTCCTACAA,AAAGAACGTCCTCAGG,AAAGAACGTCGAGCTC-1,AAAGAACGTCTCTCCA,AAAGAACGTCTGTGGC,AAAGAACGTGCAGATG,AAAGAACGTGTGATGG,AAAGAACGTGTTCAGT,AAAGAACGTTATGACC,AAAGAACGTTCAGCGC,AAAGAACGTTCTCTCG,AAAGAACGTTCTTAGG-1,AAAGAACGTTGCTCAA,AAAGAACGTTGTGCCG,AAAGAACGTTTCGACA-1,AAAGAACTCAAGAGTA,AAAGAACTCAATCGGT,AAAGAACTCAATCTTC-1,AAAGAACTCACCCTTG,AAAGAACTCACGGGAA,AAAGAACTCACTGTTT,AAAGAACTCATGGGAG,AAAGAACTCATTGGTG,AAAGAACTCCAAGAGG,AAAGAACTCCCAGGCA,AAAGAACTCCCATTTA,AAAGAACTCCCGTTCA,AAAGAACTCCCTCGTA,AAAGAACTCCGTATGA,AAAGAACTCCTCTAGC,AAAGAACTCCTTCAGC,AAAGAACTCGAACCTA,AAAGAACTCGAATCCA,AAAGAACTCGCGGACT,AAAGAACTCGCGTCGA,AAAGAACTCGCTCATC,AAAGAACTCGTAGTGT-1,AAAGAACTCGTGGACC,AAAGAACTCTCGCGTT,AAAGAACTCTGCGTCT,AAAGAACTCTGCTTAT,AAAGAACTCTTCTCAA,AAAGGATAGAACAAGG,AAAGGATA################################### QC stats performed:FALSE, PCA performed:TRUE Clustering performed:TRUE, Number of clusters:23 tSNE performed:TRUE, UMAP performed:TRUE, DiffMap performed:FALSE Main data dimensions (rows,columns): 4000,115682

Yale73 commented 4 years ago

The left Data conditions in main data:AAACCCAAGAAGTCTA,AAACCCAAGAATCGCG,AAACCCAAGAATCTAG,AAACCCAAGACACACG,AAACCCAAGACCGCCT,AAACCCAAGAGAGAAC,AAACCCAAGAGTCAGC,AAACCCAAGAGTTCGG,AAACCCAAGATGTTCC,AAACCCAAGCACGGAT,AAACCCAAGCAGGCTA,AAACCCAAGCATGTTC,AAACCCAAGCATTGAA-1,AAACCCAAGCGCTGCT,AAACCCAAGCGTATAA,AAACCCAAGCGTTCAT,AAACCCAAGCTTTGTG,AAACCCAAGGACGGAG,AAACCCAAGGATGTTA,AAACCCAAGGCAGTCA,AAACCCAAGGCTGGAT,AAACCCAAGGGACACT,AAACCCAAGGGCAGTT,AAACCCAAGGTCGTCC,AAACCCAAGGTCTTTG,AAACCCAAGGTTAAAC-1,AAACCCAAGTATGATG,AAACCCAAGTCATAGA,AAACCCAAGTCCGCGT,AAACCCAAGTCGGCAA,AAACCCAAGTGCTCGC,AAACCCAAGTGGCGAT,AAACCCAAGTTCCTGA-1,AAACCCACAACCAATC,AAACCCACAACGATTC,AAACCCACAAGTGATA,AAACCCACAAGTGGGT,AAACCCACAATACAGA,AAACCCACACGAAGAC,AAACCCACACTGCTTC,AAACCCACACTGGCCA,AAACCCACACTTGAAC,AAACCCACAGAAATCA,AAACCCACAGAGGGTT-1,AAACCCACAGAGGTAC,AAACCCACAGAGTCTT,AAACCCACAGATAAAC,AAACCCACAGCAGAAC,AAACCCACAGCGAGTA,AAACCCACAGGACTTT,AAACCCACAGGCTTGC,AAACCCACAGGTGGAT,AAACCCACAGTCCGTG,AAACCCACAGTTCTAG-1,AAACCCACATAACGGG,AAACCCACATCAGCTA,AAACCCACATCGATAC,AAACCCACATCGATCA,AAACCCACATCTGGGC,AAACCCACATGACTGT,AAACCCACATGTCTAG,AAACCCACATTAGGCT,AAACCCACATTGTACG,AAACCCAGTAACATAG,AAACCCAGTAACGTTC,AAACCCAGTAAGGTCG,AAACCCAGTACTGAGG-1,AAACCCAGTACTGTTG,AAACCCAGTACTTCCC-1,AAACCCAGTAGCCAGA,AAACCCAGTATTTCTC-1,AAACCCAGTCACCGCA,AAACCCAGTCACTCGG,AAACCCAGTCCGGACT,AAACCCAGTCGGTGTC,AAACCCAGTCGTACAT,AAACCCAGTCGTTTCC,AAACCCAGTCTCAGAT,AAACCCAGTGAGACGT,AAACCCAGTGAGTGAC,AAACCCAGTGGTATGG,AAACCCAGTGTAGGAC,AAACCCAGTGTATTCG,AAACCCAGTGTCATCA,AAACCCAGTGTGAATA,AAACCCAGTTAGAAGT,AAACCCAGTTAGGCCC,AAACCCAGTTTAAGGA,AAACCCAGTTTCACAG,AAACCCATCACACCCT,AAACCCATCACCATGA,AAACCCATCACTACTT,AAACCCATCACTAGCA,AAACCCATCAGAGTTC,AAACCCATCATGCATG-1,AAACCCATCCATGCAA,AAACCCATCCATTTCA,AAACCCATCCCAATAG,AAACCCATCCCTGGTT,AAACCCATCCGCACGA,AAACCCATCCGGTAGC,AAACCCATCCGTGTAA,AAACCCATCCTACAAG,AAACCCATCCTACGAA,AAACCCATCCTGCCAT,AAACCCATCCTGTTAT,AAACCCATCCTTATGT,AAACCCATCGAGATAA,AAACCCATCGAGTACT,AAACCCATCGCCAATA,AAACCCATCGGCCCAA,AAACCCATCGGTAGAG-1,AAACCCATCGGTCATA,AAACCCATCGTAGCTA,AAACCCATCTAAGCCA,AAACCCATCTCACCCA,AAACCCATCTCCTGTG,AAACCCATCTGCTGAA,AAACCCATCTGTGCTC,AAACCCATCTTAGCAG,AAACCCATCTTAGTTC,AAACCCATCTTCCCAG,AAACCCATCTTCTCAA,AAACCCATCTTTCCGG,AAACGAAAGACGGATC,AAACGAAAGAGAACCC,AAACGAAAGAGGACTC,AAACGAAAGAGTCACG,AAACGAAAGATCACTC,AAACGAAAGATCCGAG,AAACGAAAGATTTGCC,AAACGAAAGCAGGCTA,AAACGAAAGCATGCGA,AAACGAAAGCCTGAGA,AAACGAAAGCGACCCT,AAACGAAAGCTGACCC,AAACGAAAGCTGACTT,AAACGAAAGCTGAGTG,AAACGAAAGCTTCTAG,AAACGAAAGGACCCAA,AAACGAAAGGACTGGT,AAACGAAAGGCTTCCG,AAACGAAAGGGATCAC,AAACGAAAGGGCATGT,AAACGAAAGGGCCAAT,AAACGAAAGGGTACGT,AAACGAAAGGGTTAGC,AAACGAAAGGTACCTT,AAACGAAAGGTGCTTT,AAACGAAAGGTTGGAC,AAACGAAAGTATTCCG,AAACGAAAGTCTCCTC,AAACGAAAGTGAGTTA,AAACGAAAGTTACGTC,AAACGAAAGTTGGCGA,AAACGAAAGTTGGCTT,AAACGAACAAACTGCT,AAACGAACAAAGGGTC,AAACGAACAAAGGTTA,AAACGAACAAATTGGA,AAACGAACAACACAAA,AAACGAACAACGCCCA-1,AAACGAACAACTCGAT,AAACGAACAATAGTAG,AAACGAACAATCACGT,AAACGAACACACCGCA,AAACGAACACACCTAA,AAACGAACACCATATG,AAACGAACACCATTCC,AAACGAACACCGTGGT,AAACGAACACGCGCTA,AAACGAACACGGTGTC,AAACGAACACTGTCGG,AAACGAACAGAACCGA,AAACGAACAGAGGGTT,AAACGAACAGATCACT,AAACGAACAGCCTTCT,AAACGAACAGGATGAC-1,AAACGAACAGTTGTTG,AAACGAACATACCAGT,AAACGAACATATCTGG,AAACGAACATCATCCC,AAACGAACATCATTTC,AAACGAACATCCGAGC,AAACGAACATCGCTAA-1,AAACGAACATGAATCC,AAACGAACATGACGAG,AAACGAACATGCAGCC,AAACGAACATGCTGCG,AAACGAACATGTGCCG,AAACGAACATTGACCA,AAACGAAGTACAAAGT,AAACGAAGTACCGCGT,AAACGAAGTACCGGAA,AAACGAAGTAGAAACT,AAACGAAGTAGAATGT,AAACGAAGTAGACGGT,AAACGAAGTAGTCGTT,AAACGAAGTATCAAGA,AAACGAAGTCACTTAG,AAACGAAGTCCCACGA,AAACGAAGTCGTAATC,AAACGAAGTCTACATG-1,AAACGAAGTCTACTGA,AAACGAAGTCTATGAC,AAACGAAGTCTGCAAT,AAACGAAGTCTGCCTT,AAACGAAGTCTGTCAA,AAACGAAGTCTTGTCC,AAACGAAGTGCACATT,AAACGAAGTGCATCTA,AAACGAAGTGCCCAGT-1,AAACGAAGTGCGTTTA,AAACGAAGTGGGTCAA,AAACGAAGTTGAGGAC,AAACGAAGTTGTGTAC,AAACGAAGTTTACCTT,AAACGAATCAACCCGG,AAACGAATCAACTGAC,AAACGAATCAATGTCG,AAACGAATCACTCACC,AAACGAATCAGCACCG,AAACGAATCAGCTCTC,AAACGAATCAGGTGTT,AAACGAATCATGAAAG,AAACGAATCCACACAA,AAACGAATCCATTGGA,AAACGAATCCTGATAG,AAACGAATCGAACCTA,AAACGAATCGAATCCA,AAACGAATCGAGGCAA,AAACGAATCGCGGACT,AAACGAATCGCGTAGC,AAACGAATCGCTAAAC,AAACGAATCGCTTTAT,AAACGAATCGGACAAG,AAACGAATCGGTATGT,AAACGAATCGTCAAAC,AAACGAATCGTTATCT,AAACGAATCTACTTCA,AAACGAATCTCGACCT,AAACGAATCTGGTGGC,AAACGAATCTTCCAGC,AAACGAATCTTTACAC,AAACGCTAGAATACAC,AAACGCTAGAATCGCG,AAACGCTAGACCGCCT-1,AAACGCTAGAGATTCA,AAACGCTAGAGCAAGA,AAACGCTAGAGCAGAA,AAACGCTAGATAACAC,AAACGCTAGATGACAT,AAACGCTAGATGGCGT,AAACGCTAGCAACCAG,AAACGCTAGCCAGACA,AAACGCTAGCCATATC,AAACGCTAGCCATTTG,AAACGCTAGGAACTAT,AAACGCTAGGACAACC,AAACGCTAGGATTCAA,AAACGCTAGGCACCAA,AAACGCTAGGCAGGGA,AAACGCTAGGCCGCTT,AAACGCTAGGCTCAAG,AAACGCTAGGGCGAAG,AAACGCTAGGTAGCCA,AAACGCTAGGTCTGGA,AAACGCTAGGTTACAA,AAACGCTAGTAAGCAT,AAACGCTAGTACTGTC-1,AAACGCTAGTATGATG,AAACGCTAGTCGAAGC,AAACGCTAGTGCTACT-1,AAACGCTAGTGGCAGT,AAACGCTAGTTCCATG,AAACGCTAGTTGCATC-1,AAACGCTAGTTGTAGA,AAACGCTCAAACGGCA,AAACGCTCAAAGGCGT,AAACGCTCAAATCAGA-1,AAACGCTCAACGACAG,AAACGCTCAACTGATC,AAACGCTCAAGCAATA,AAACGCTCAAGTGGCA,AAACGCTCAATCTCTT,AAACGCTCAATGAACA,AAACGCTCAATTCTTC,AAACGCTCACACCAGC,AAACGCTCACCGTGAC,AAACGCTCACGGCACT,AAACGCTCACTACCGG-1,AAACGCTCACTATCGA,AAACGCTCACTCCGAG,AAACGCTCACTGGCGT,AAACGCTCACTTACAG,AAACGCTCACTTGAAC,AAACGCTCAGAGAAAG,AAACGCTCAGAGGACT-1,AAACGCTCAGAGTCTT,AAACGCTCAGATGCGA,AAACGCTCAGCCCAGT,AAACGCTCAGCGTACC,AAACGCTCAGGCACTC,AAACGCTCAGGGCTTC,AAACGCTCAGTAACCT,AAACGCTCATAACTCG,AAACGCTCATACTGAC,AAACGCTCATAGGCGA,AAACGCTCATCCTTCG,AAACGCTCATCTAGAC,AAACGCTCATGGCCAC,AAACGCTCATTGGGAG,AAACGCTGTACGTAGG,AAACGCTGTACTCAAC,AAACGCTGTAGAATGT,AAACGCTGTAGACAAT,AAACGCTGTAGTACGG,AAACGCTGTCCTTGTC,AAACGCTGTCGAGTTT,AAACGCTGTGATTAGA,AAACGCTGTGCAGATG,AAACGCTGTGCCGAAA,AAACGCTGTGCGCTCA,AAACGCTGTGGATACG,AAACGCTGTGGATGAC-1,AAACGCTGTGTCATGT,AAACGCTGTGTCGCTG,AAACGCTGTGTGCTTA,AAACGCTGTTAAGACA,AAACGCTGTTACGATC,AAACGCTGTTAGGCTT,AAACGCTGTTCAAGGG,AAACGCTGTTCCCACT,AAACGCTGTTCGGACC,AAACGCTGTTTACGAC,AAACGCTTCAAGTCGT,AAACGCTTCAATCAGC,AAACGCTTCAATCCAG,AAACGCTTCAATCTCT,AAACGCTTCACGAACT,AAACGCTTCACTAGCA,AAACGCTTCAGGTGTT,AAACGCTTCAGTAGGG,AAACGCTTCATAGACC,AAACGCTTCATCGCTC,AAACGCTTCATCTATC,AAACGCTTCATGAGGG-1,AAACGCTTCATGGGAG,AAACGCTTCCACATAG,AAACGCTTCCACGAAT,AAACGCTTCCATCCGT,AAACGCTTCCATTGTT,AAACGCTTCCGAGAAG,AAACGCTTCCGAGTGC,AAACGCTTCCGGCAAC,AAACGCTTCCGTCAAA,AAACGCTTCCTCATAT,AAACGCTTCGACCACG,AAACGCTTCGACGACC-1,AAACGCTTCGCTTAAG,AAACGCTTCGGCTGAC,AAACGCTTCGGTGCAC,AAACGCTTCGTTCTCG,AAACGCTTCTACAGGT,AAACGCTTCTACGGGC,AAACGCTTCTATGCCC,AAACGCTTCTATTCGT,AAACGCTTCTCCGATC,AAACGCTTCTCGAACA,AAACGCTTCTCGCTCA,AAACGCTTCTCTCTTC,AAACGCTTCTGTGCAA,AAACGCTTCTTACCGC,AAACGCTTCTTAGGAC,AAACGCTTCTTTCAGT,AAAGAACAGAAGCTCG,AAAGAACAGACCAAAT,AAAGAACAGAGCATAT,AAAGAACAGATCCCGC,AAAGAACAGCCGAACA,AAAGAACAGCCGAATG,AAAGAACAGCGCCTCA,AAAGAACAGGACAGCT,AAAGAACAGGATTTAG,AAAGAACAGGATTTCC,AAAGAACAGGGTTGCA,AAAGAACAGGTATCTC,AAAGAACAGTAACGTA,AAAGAACAGTACAACA,AAAGAACAGTCCCAAT,AAAGAACAGTCGTCTA,AAAGAACAGTCTTCGA,AAAGAACAGTTGAAGT-1,AAAGAACCAAAGTGTA,AAAGAACCAAGCCCAC,AAAGAACCAATCAGCT,AAAGAACCAATCTCGA,AAAGAACCAATCTGCA,AAAGAACCACAGTATC,AAAGAACCACCCGTAG,AAAGAACCACCCTAAA,AAAGAACCACGCCAGT,AAAGAACCAGAAATTG,AAAGAACCAGACAAGC,AAAGAACCAGACCAGA-1,AAAGAACCAGACCTGC,AAAGAACCAGCAGTCC,AAAGAACCAGCCTATA,AAAGAACCAGGCTATT,AAAGAACCAGTAGTTC,AAAGAACCATCTATCT,AAAGAACCATGAGAAT,AAAGAACCATGCAGGA,AAAGAACCATTGACTG,AAAGAACGTAACGATA-1,AAAGAACGTACAAGCG,AAAGAACGTACCCGAC,AAAGAACGTACCCGCA,AAAGAACGTACGTAGG,AAAGAACGTACTCCCT,AAAGAACGTACTCGTA,AAAGAACGTAGGCAAC,AAAGAACGTAGGTTTC,AAAGAACGTAGTCTGT,AAAGAACGTATGACAA,AAAGAACGTCAGTTTG,AAAGAACGTCATAAAG,AAAGAACGTCCTACAA,AAAGAACGTCCTCAGG,AAAGAACGTCGAGCTC-1,AAAGAACGTCTCTCCA,AAAGAACGTCTGTGGC,AAAGAACGTGCAGATG,AAAGAACGTGTGATGG,AAAGAACGTGTTCAGT,AAAGAACGTTATGACC,AAAGAACGTTCAGCGC,AAAGAACGTTCTCTCG,AAAGAACGTTCTTAGG-1,AAAGAACGTTGCTCAA,AAAGAACGTTGTGCCG,AAAGAACGTTTCGACA-1,AAAGAACTCAAGAGTA,AAAGAACTCAATCGGT,AAAGAACTCAATCTTC-1,AAAGAACTCACCCTTG,AAAGAACTCACGGGAA,AAAGAACTCACTGTTT,AAAGAACTCATGGGAG,AAAGAACTCATTGGTG,AAAGAACTCCAAGAGG,AAAGAACTCCCAGGCA,AAAGAACTCCCATTTA,AAAGAACTCCCGTTCA,AAAGAACTCCCTCGTA,AAAGAACTCCGTATGA,AAAGAACTCCTCTAGC,AAAGAACTCCTTCAGC,AAAGAACTCGAACCTA,AAAGAACTCGAATCCA,AAAGAACTCGCGGACT,AAAGAACTCGCGTCGA,AAAGAACTCGCTCATC,AAAGAACTCGTAGTGT-1,AAAGAACTCGTGGACC,AAAGAACTCTCGCGTT,AAAGAACTCTGCGTCT,AAAGAACTCTGCTTAT,AAAGAACTCTTCTCAA,AAAGGATAGAACAAGG,AAAGGATAGAACCCGA,AAAGGATAGACCAGCA,AAAGGATAGACCTCCG,AAAGGATAGACGGATC,AAAGGATAGACTGAGC,AAAGGATAGAGCATCG,A Normalization factors:,... Imputed data dimensions (rows,columns):0,0 ############## scVDJ-seq ########### VDJ data dimentions (rows,columns):0,0 ############## CITE-seq ############ ADT raw data dimensions (rows,columns):0,0 ADT main data dimensions (rows,columns):0,0 ADT columns names:... ADT row names:... ############## scATAC-seq ############ ATAC raw data dimensions (rows,columns):0,0 ATAC main data dimensions (rows,columns):0,0 ATAC columns names:... ATAC row names:... ############## Spatial ########### Spatial data dimentions (rows,columns):0,0 ########### iCellR object ##########

rezakj commented 4 years ago

I am bit busy but now, but to solve it faster why don't you just run the analysis in iCellR from the start and if you like the clusters from the old analysis keep the same numbers. But we can look into it later to see where the issue is.