Closed yueli8 closed 6 months ago
ncborcherding
commented
6 months ago Hey Yue,
Would you mind making a reproducible example for this issue?
It looks like the function works for at least one element of combinedTCR - but not all - so the issue may be in the list elements. Do all the elements of the combinedTCR have contig information?
Thanks, Nick
yueli8
commented
6 months ago Hello Nike,
Thank you so much for your quick response!
Unfortunately, it still does not work.
I worked with scRepertoire on version 2.0.3. It works well onpositionalEntropy, but does
not on positionalProperty.
Thank you in advance for your great help!
Please see attached files.
Best,
Yue
rm(list=ls())
library(immunarch)
library(scRepertoire)
library(tidyverse)
library(SingleCellExperiment)
library(Seurat)
library(powerTCR)
read_mixcr_n_trans<- function(file,...){
df <- read.delim(file)
# transform the cell id {be consist with RNA data}
{
well<- gsub(df$tagValueCELL,pattern = "[AGCT]*-",replacement = "")
hp<- gsub(df$tagValueCELL,pattern = "-[AGCT]*-.*",replacement = "")
rt<- str_extract(df$tagValueCELL,pattern = "-[AGCT]{10}")%>%
str_sub(.,start = 2,end = nchar(.))
}
# add a column named "tagValueCELL" {as normal mixcr output}
df$tagValueCELL<- paste(well,hp,rt,sep ="_" )
return(df)
}
#four samples# Step1: Load MIXCR output -----------------------------------------
TIL_4095_1 <- "TIL_4095_101.csv"
TIL_4095_2 <- "TIL_4095_201.csv"
TIL_4095_3 <- "TIL_4095_301.csv"
TIL_4095_4 <- "TIL_4095_401.csv"
filelist <- c(TIL_4095_1,TIL_4095_2,TIL_4095_3,TIL_4095_4)
samples <- c("S1","S2","S3","S4")
contig_list<- lapply(filelist, function(x) read_mixcr_n_trans(x))
colnames(contig_list[[1]])
# convert to "scRepertoire" style
contig.list <- loadContigs(contig_list, format = "MiXCR")
#combineTCR
combined.TCR <- combineTCR(contig.list,
samples = samples,
removeNA = FALSE,
removeMulti = FALSE,
filterMulti = FALSE)
positionalEntropy(combined.TCR,
chain = "TRB",
aa.length = 20)
#positionalProperty
positionalProperty(combined.TCR[c(1,2)],
chain = "TRB",
aa.length = 20,
method = "Atchley") +
scale_color_manual(values = hcl.colors(5, "inferno"))
Error in propertyFunc[char, ] : subscript out of bounds
In addition: Warning message:
In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
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_US.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] powerTCR_1.20.0 SeuratObject_4.1.4 Seurat_4.4.0 SingleCellExperiment_1.22.0
[5] SummarizedExperiment_1.30.2 GenomicRanges_1.52.1 GenomeInfoDb_1.36.4 IRanges_2.36.0
[9] S4Vectors_0.40.2 MatrixGenerics_1.12.3 matrixStats_1.3.0 lubridate_1.9.3
[13] forcats_1.0.0 stringr_1.5.1 purrr_1.0.2 readr_2.1.5
[17] tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0 scRepertoire_2.0.3
[21] immunarch_0.9.1 patchwork_1.2.0 data.table_1.15.4 dtplyr_1.3.1
[25] dplyr_1.1.4 ggplot2_3.5.1 bigmemory_4.6.4 Biobase_2.60.0
[29] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-3 bitops_1.0-7 httr_1.4.7 RColorBrewer_1.1-3 doParallel_1.0.17
[6] prabclus_2.3-3 tools_4.3.0 sctransform_0.4.1 backports_1.4.1 vegan_2.6-4
[11] utf8_1.2.4 R6_2.5.1 mgcv_1.9-1 lazyeval_0.2.2 uwot_0.2.2
[16] permute_0.9-7 GetoptLong_1.0.5 withr_3.0.0 sp_2.1-4 gridExtra_2.3
[21] progressr_0.14.0 quantreg_5.97 cli_3.6.2 factoextra_1.0.7 spatstat.explore_3.2-7
[26] iNEXT_3.0.1 network_1.18.2 labeling_0.4.3 diptest_0.77-1 robustbase_0.99-2
[31] spatstat.data_3.0-4 ggridges_0.5.6 pbapply_1.7-2 systemfonts_1.0.6 svglite_2.1.3
[36] stringdist_0.9.12 parallelly_1.37.1 readxl_1.4.3 VGAM_1.1-10 rstudioapi_0.16.0
[41] FNN_1.1.4 generics_0.1.3 shape_1.4.6.1 ica_1.0-3 spatstat.random_3.2-3
[46] car_3.1-2 Matrix_1.6-1.1 fansi_1.0.6 abind_1.4-5 lifecycle_1.0.4
[51] carData_3.0-5 Rtsne_0.17 grid_4.3.0 promises_1.3.0 crayon_1.5.2
[56] miniUI_0.1.1.1 lattice_0.22-6 cowplot_1.1.3 sna_2.7-2 pillar_1.9.0
[61] ComplexHeatmap_2.16.0 rjson_0.2.21 fpc_2.2-12 CellChat_1.6.1 future.apply_1.11.2
[66] codetools_0.2-20 fastmatch_1.1-4 leiden_0.4.3.1 glue_1.7.0 vctrs_0.6.5
[71] png_0.1-8 cellranger_1.1.0 gtable_0.3.5 kernlab_0.9-32 cachem_1.0.8
[76] S4Arrays_1.2.1 mime_0.12 tidygraph_1.3.1 coda_0.19-4.1 survival_3.6-4
[81] pheatmap_1.0.12 iterators_1.0.14 shinythemes_1.2.0 fitdistrplus_1.1-11 ROCR_1.0-11
[86] nlme_3.1-164 RcppAnnoy_0.0.22 evd_2.3-7 UpSetR_1.4.0 irlba_2.3.5.1
[91] KernSmooth_2.23-22 colorspace_2.1-0 nnet_7.3-19 phangorn_2.11.1 tidyselect_1.2.1
[96] compiler_4.3.0 BiocNeighbors_1.18.0 SparseM_1.81 ggdendro_0.2.0 DelayedArray_0.26.7
[101] plotly_4.10.4 scales_1.3.0 DEoptimR_1.1-3 lmtest_0.9-40 quadprog_1.5-8
[106] NMF_0.27 digest_0.6.35 goftest_1.2-3 spatstat.utils_3.0-4 XVector_0.40.0
[111] htmltools_0.5.8.1 pkgconfig_2.0.3 fastmap_1.1.1 rlang_1.1.3 GlobalOptions_0.1.2
[116] htmlwidgets_1.6.4 shiny_1.8.1.1 farver_2.1.1 zoo_1.8-12 jsonlite_1.8.8
[121] BiocParallel_1.34.2 mclust_6.1.1 statnet.common_4.9.0 RCurl_1.98-1.14 rlist_0.4.6.2
[126] magrittr_2.0.3 modeltools_0.2-23 GenomeInfoDbData_1.2.10 ggnetwork_0.5.13 evmix_2.12
[131] munsell_0.5.1 Rcpp_1.0.12 ape_5.8 viridis_0.6.5 reticulate_1.36.1
[136] truncdist_1.0-2 stringi_1.8.4 ggalluvial_0.12.5 ggraph_2.2.1 zlibbioc_1.46.0
[141] MASS_7.3-60 plyr_1.8.9 flexmix_2.3-19 ggseqlogo_0.2 parallel_4.3.0
[146] listenv_0.9.1 ggrepel_0.9.5 bigmemory.sri_0.1.8 deldir_2.0-4 graphlayouts_1.1.1
[151] splines_4.3.0 hash_2.2.6.3 tensor_1.5 hms_1.1.3 circlize_0.4.16
[156] igraph_2.0.3 ggpubr_0.6.0 uuid_1.2-0 cubature_2.1.0 spatstat.geom_3.2-9
[161] ggsignif_0.6.4 rngtools_1.5.2 reshape2_1.4.4 BiocManager_1.30.23 tzdb_0.4.0
[166] foreach_1.5.2 tweenr_2.0.3 httpuv_1.6.15 MatrixModels_0.5-3 RANN_2.6.1
[171] polyclip_1.10-6 future_1.33.2 clue_0.3-65 scattermore_1.2 gridBase_0.4-7
[176] ggforce_0.4.2 broom_1.0.5 xtable_1.8-4 RSpectra_0.16-1 rstatix_0.7.2
[181] later_1.3.2 viridisLite_0.4.2 class_7.3-22 gsl_2.1-8 memoise_2.0.1
[186] registry_0.5-1 cluster_2.1.6 timechange_0.3.0 globals_0.16.3 TIL_4095_101.csv.csv TIL_4095_201.csv.csv TIL_4095_301.csv.csv TIL_4095_401.csv.csv
ncborcherding
commented
6 months ago @yueli8
Thank you so much for the excellent run down. I was able to reproduce the issue and fix it - I have slightly modified the code below - you can just your lapply(filelist, read.delim) and then use loadContigs().
#four samples# Step1: Load MIXCR output -----------------------------------------
TIL_4095_1 <- "TIL_4095_101.csv"
TIL_4095_2 <- "TIL_4095_201.csv"
TIL_4095_3 <- "TIL_4095_301.csv"
TIL_4095_4 <- "TIL_4095_401.csv"
filelist <- c(TIL_4095_1,TIL_4095_2,TIL_4095_3,TIL_4095_4)
samples <- c("S1","S2","S3","S4")
contig_list <- lapply(filelist, read.delim)
contig.list <- loadContigs(contig_list, format = "MiXCR")
#combineTCR
combined.TCR <- combineTCR(contig.list,
samples = samples,
removeNA = FALSE,
removeMulti = FALSE,
filterMulti = FALSE)
positionalEntropy(combined.TCR,
chain = "TRB",
aa.length = 20)
#positionalProperty
positionalProperty(combined.TCR,
chain = "TRB",
aa.length = 20,
method = "Atchley") +
scale_color_manual(values = hcl.colors(5, "inferno"))The issue was that positionalProperty() expected all amino acids to be present. Across your 4 samples, there are several where not all 20 amino acids are present, so the error occured.
I have commited the fix to the dev branch of the repo and I will test it out and pull it into the master branch in the coming weeks.
Thanks again for following up, Nick
yueli8
commented
6 months ago Hello Nike,
Thank you so much for your detail explanation!
Unfortunately, it does not work on my system.
Thank you again and really appreciated!
Best,
Yue
rm(list=ls())
library(immunarch)
library(scRepertoire)
library(tidyverse)
library(SingleCellExperiment)
library(Seurat)
library(powerTCR)
TIL_4095_1 <- "TIL_4095_101.csv"
TIL_4095_2 <- "TIL_4095_201.csv"
TIL_4095_3 <- "TIL_4095_301.csv"
TIL_4095_4 <- "TIL_4095_401.csv"
filelist <- c(TIL_4095_1,TIL_4095_2,TIL_4095_3,TIL_4095_4)
samples <- c("S1","S2","S3","S4")
contig_list <- lapply(filelist, read.delim)
contig.list <- loadContigs(contig_list, format = "MiXCR")
#combineTCR
combined.TCR <- combineTCR(contig.list,
samples = samples,
removeNA = FALSE,
removeMulti = FALSE,
filterMulti = FALSE)
positionalEntropy(combined.TCR,
chain = "TRB",
aa.length = 20)
Warning messages:
1: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
2: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
3: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
4: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
#positionalProperty
positionalProperty(combined.TCR,
chain = "TRB",
aa.length = 20,
method = "Atchley") +
scale_color_manual(values = hcl.colors(5, "inferno"))
Error in propertyFunc[char, ] : subscript out of bounds
In addition: Warning messages:
1: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
2: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
3: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
4: In `[<-.factor`(`*tmp*`, thisvar, value = 0) :
invalid factor level, NA generated
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
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_US.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] powerTCR_1.20.0 SeuratObject_4.1.4 Seurat_4.4.0 SingleCellExperiment_1.22.0
[5] SummarizedExperiment_1.30.2 Biobase_2.60.0 GenomicRanges_1.52.1 GenomeInfoDb_1.36.4
[9] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1 MatrixGenerics_1.12.3
[13] matrixStats_1.3.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[17] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[21] tidyverse_2.0.0 scRepertoire_2.0.3 immunarch_0.9.1 patchwork_1.2.0
[25] data.table_1.15.4 dtplyr_1.3.1 dplyr_1.1.4 ggplot2_3.5.1
loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-3 bitops_1.0-7 httr_1.4.7 RColorBrewer_1.1-3 doParallel_1.0.17
[6] prabclus_2.3-3 tools_4.3.0 sctransform_0.4.1 backports_1.4.1 vegan_2.6-4
[11] utf8_1.2.4 R6_2.5.1 mgcv_1.9-1 lazyeval_0.2.2 uwot_0.2.2
[16] permute_0.9-7 withr_3.0.0 sp_2.1-4 gridExtra_2.3 progressr_0.14.0
[21] quantreg_5.97 cli_3.6.2 factoextra_1.0.7 spatstat.explore_3.2-7 iNEXT_3.0.1
[26] labeling_0.4.3 diptest_0.77-1 robustbase_0.99-2 spatstat.data_3.0-4 ggridges_0.5.6
[31] pbapply_1.7-2 stringdist_0.9.12 parallelly_1.37.1 readxl_1.4.3 VGAM_1.1-10
[36] rstudioapi_0.16.0 generics_0.1.3 shape_1.4.6.1 ica_1.0-3 spatstat.random_3.2-3
[41] car_3.1-2 Matrix_1.6-1.1 fansi_1.0.6 abind_1.4-5 lifecycle_1.0.4
[46] carData_3.0-5 Rtsne_0.17 grid_4.3.0 promises_1.3.0 crayon_1.5.2
[51] miniUI_0.1.1.1 lattice_0.22-6 cowplot_1.1.3 pillar_1.9.0 rjson_0.2.21
[56] fpc_2.2-12 future.apply_1.11.2 codetools_0.2-20 fastmatch_1.1-4 leiden_0.4.3.1
[61] glue_1.7.0 vctrs_0.6.5 png_0.1-8 cellranger_1.1.0 gtable_0.3.5
[66] kernlab_0.9-32 cachem_1.0.8 S4Arrays_1.2.1 mime_0.12 tidygraph_1.3.1
[71] survival_3.6-4 pheatmap_1.0.12 iterators_1.0.14 shinythemes_1.2.0 fitdistrplus_1.1-11
[76] ROCR_1.0-11 nlme_3.1-164 RcppAnnoy_0.0.22 evd_2.3-7 UpSetR_1.4.0
[81] irlba_2.3.5.1 KernSmooth_2.23-22 colorspace_2.1-0 nnet_7.3-19 phangorn_2.11.1
[86] tidyselect_1.2.1 compiler_4.3.0 SparseM_1.81 ggdendro_0.2.0 DelayedArray_0.26.7
[91] plotly_4.10.4 scales_1.3.0 DEoptimR_1.1-3 lmtest_0.9-40 quadprog_1.5-8
[96] digest_0.6.35 goftest_1.2-3 spatstat.utils_3.0-4 XVector_0.40.0 htmltools_0.5.8.1
[101] pkgconfig_2.0.3 fastmap_1.1.1 rlang_1.1.3 GlobalOptions_0.1.2 htmlwidgets_1.6.4
[106] shiny_1.8.1.1 farver_2.1.1 zoo_1.8-12 jsonlite_1.8.8 mclust_6.1.1
[111] RCurl_1.98-1.14 rlist_0.4.6.2 magrittr_2.0.3 modeltools_0.2-23 GenomeInfoDbData_1.2.10
[116] munsell_0.5.1 Rcpp_1.0.12 evmix_2.12 ape_5.8 viridis_0.6.5
[121] reticulate_1.36.1 truncdist_1.0-2 stringi_1.8.4 ggalluvial_0.12.5 ggraph_2.2.1
[126] zlibbioc_1.46.0 MASS_7.3-60 plyr_1.8.9 flexmix_2.3-19 ggseqlogo_0.2
[131] parallel_4.3.0 listenv_0.9.1 ggrepel_0.9.5 deldir_2.0-4 graphlayouts_1.1.1
[136] splines_4.3.0 hash_2.2.6.3 tensor_1.5 hms_1.1.3 circlize_0.4.16
[141] igraph_2.0.3 ggpubr_0.6.0 uuid_1.2-0 spatstat.geom_3.2-9 cubature_2.1.0
[146] ggsignif_0.6.4 reshape2_1.4.4 tzdb_0.4.0 foreach_1.5.2 tweenr_2.0.3
[151] httpuv_1.6.15 MatrixModels_0.5-3 RANN_2.6.1 polyclip_1.10-6 future_1.33.2
[156] scattermore_1.2 ggforce_0.4.2 broom_1.0.5 xtable_1.8-4 rstatix_0.7.2
[161] later_1.3.2 viridisLite_0.4.2 class_7.3-22 gsl_2.1-8 memoise_2.0.1
[166] cluster_2.1.6 timechange_0.3.0 globals_0.16.3
Hello ncborcherding,
I worked with
scRepertoireon version2.0.3. It works well onpositionalEntropy, but not onpositionalProperty.Thank you in advance for great help!
Best,
Yue