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annotation attribute in CoveragePlot function #1294

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pengxin2019 opened this issue Nov 28, 2022 · 7 comments
Closed

annotation attribute in CoveragePlot function #1294

pengxin2019 opened this issue Nov 28, 2022 · 7 comments
Labels
bug Something isn't working
Milestone
1.9.0

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@pengxin2019
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Hi Signac team,
I have an Seurat object and its information is here:
Here is the description of my Seurat object integrated which was annotated using a gtf file

> integrated
An object of class Seurat 
130479 features across 15626 samples within 2 assays 
Active assay: peaks (110444 features, 110272 variable features)
 1 other assay present: RNA
 3 dimensional reductions calculated: integrated_lsi, umap, lsi

I was trying to set annotation="transcript" for CoveragePlot function in oder to plot all transcripts in gene track since you mentioned that the longest transcript is used by default. However, I found this error below. Can you give me some comments?

 p <- CoveragePlot(
  object = integrated,
  region = "2-151108982-151113383",#
  extend.upstream = 20000,
  extend.downstream = 20000,
  show.bulk = TRUE,
  ranges = ranges.show,
  region.highlight = ranges.show,
  annotation = "transcript"
)

error:
Error in if (annotation) { : argument is not interpretable as logical
The annotation of this Seurat object look like this:

> Annotation(integrated)
GRanges object with 1530978 ranges and 21 metadata columns:
                  seqnames    ranges strand |   source       type     score
                     <Rle> <IRanges>  <Rle> | <factor>   <factor> <numeric>
        [1]              1    1-3782      + |  ensembl gene              NA
        [2]              1    1-3780      + |  ensembl transcript        NA
        [3]              1    1-2465      + |  ensembl exon              NA
        [4]              1 3118-3780      + |  ensembl exon              NA
        [5]              1  792-3782      + |  ensembl transcript        NA
        ...            ...       ...    ... .      ...        ...       ...
  [1530974] AEMK02000302.1 5535-5587      - |  ensembl exon              NA
  [1530975] AEMK02000302.1      4-47      - |  ensembl exon              NA
  [1530976] AEMK02000302.1    4-8300      - |  ensembl transcript        NA
  [1530977] AEMK02000302.1 8159-8300      - |  ensembl exon              NA
  [1530978] AEMK02000302.1      4-47      - |  ensembl exon              NA
                phase            gene_id gene_version gene_source gene_biotype
            <integer>        <character>  <character> <character>  <character>
        [1]      <NA> ENSSSCG00000048769            1     ensembl       lncRNA
        [2]      <NA> ENSSSCG00000048769            1     ensembl       lncRNA
        [3]      <NA> ENSSSCG00000048769            1     ensembl       lncRNA
        [4]      <NA> ENSSSCG00000048769            1     ensembl       lncRNA
        [5]      <NA> ENSSSCG00000048769            1     ensembl       lncRNA
        ...       ...                ...          ...         ...          ...
  [1530974]      <NA> ENSSSCG00000049924            1     ensembl       lncRNA
  [1530975]      <NA> ENSSSCG00000049924            1     ensembl       lncRNA
  [1530976]      <NA> ENSSSCG00000049924            1     ensembl       lncRNA
  [1530977]      <NA> ENSSSCG00000049924            1     ensembl       lncRNA
  [1530978]      <NA> ENSSSCG00000049924            1     ensembl       lncRNA
                 transcript_id transcript_version transcript_source
                   <character>        <character>       <character>
        [1]               <NA>               <NA>              <NA>
        [2] ENSSSCT00000066540                  1           ensembl
        [3] ENSSSCT00000066540                  1           ensembl
        [4] ENSSSCT00000066540                  1           ensembl
        [5] ENSSSCT00000078085                  1           ensembl
        ...                ...                ...               ...
  [1530974] ENSSSCT00000066525                  1           ensembl
  [1530975] ENSSSCT00000066525                  1           ensembl
  [1530976] ENSSSCT00000068345                  1           ensembl
  [1530977] ENSSSCT00000068345                  1           ensembl
  [1530978] ENSSSCT00000068345                  1           ensembl
            transcript_biotype exon_number            exon_id exon_version
                   <character> <character>        <character>  <character>
        [1]               <NA>        <NA>               <NA>         <NA>
        [2]             lncRNA        <NA>               <NA>         <NA>
        [3]             lncRNA           1 ENSSSCE00000399651            1
        [4]             lncRNA           2 ENSSSCE00000450299            1
        [5]             lncRNA        <NA>               <NA>         <NA>
        ...                ...         ...                ...          ...
  [1530974]             lncRNA           2 ENSSSCE00000399377            1
  [1530975]             lncRNA           3 ENSSSCE00000418429            1
  [1530976]             lncRNA        <NA>               <NA>         <NA>
  [1530977]             lncRNA           1 ENSSSCE00000453271            1
  [1530978]             lncRNA           2 ENSSSCE00000418429            1
             protein_id protein_version   gene_name transcript_name
            <character>     <character> <character>     <character>
        [1]        <NA>            <NA>        <NA>            <NA>
        [2]        <NA>            <NA>        <NA>            <NA>
        [3]        <NA>            <NA>        <NA>            <NA>
        [4]        <NA>            <NA>        <NA>            <NA>
        [5]        <NA>            <NA>        <NA>            <NA>
        ...         ...             ...         ...             ...
  [1530974]        <NA>            <NA>        <NA>            <NA>
  [1530975]        <NA>            <NA>        <NA>            <NA>
  [1530976]        <NA>            <NA>        <NA>            <NA>
  [1530977]        <NA>            <NA>        <NA>            <NA>
  [1530978]        <NA>            <NA>        <NA>            <NA>
            projection_parent_transcript         tag
                             <character> <character>
        [1]                         <NA>        <NA>
        [2]                         <NA>        <NA>
        [3]                         <NA>        <NA>
        [4]                         <NA>        <NA>
        [5]                         <NA>        <NA>
        ...                          ...         ...
  [1530974]                         <NA>        <NA>
  [1530975]                         <NA>        <NA>
  [1530976]                         <NA>        <NA>
  [1530977]                         <NA>        <NA>
  [1530978]                         <NA>        <NA>
  -------
  seqinfo: 351 sequences from an unspecified genome; no seqlengths

Here is the sessionInfo():

>  sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04 LTS

Matrix products: default
BLAS/LAPACK: /opt/miniconda3/envs/r4/lib/libopenblasp-r0.3.10.so

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

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

other attached packages:
 [1] dplyr_1.0.7         patchwork_1.1.1     ggplot2_3.3.5      
 [4] GenomeInfoDb_1.26.7 IRanges_2.24.1      S4Vectors_0.28.1   
 [7] BiocGenerics_0.36.1 SeuratObject_4.0.2  Seurat_4.0.5       
[10] Signac_1.4.0       

loaded via a namespace (and not attached):
  [1] Rtsne_0.15             colorspace_2.0-2       deldir_1.0-6          
  [4] ellipsis_0.3.2         ggridges_0.5.3         lsa_0.73.2            
  [7] XVector_0.30.0         GenomicRanges_1.42.0   spatstat.data_2.1-0   
 [10] farver_2.1.0           leiden_0.3.9           listenv_0.8.0         
 [13] SnowballC_0.7.0        ggrepel_0.9.1          fansi_0.5.0           
 [16] codetools_0.2-18       splines_4.0.5          docopt_0.7.1          
 [19] RcppRoll_0.3.0         polyclip_1.10-0        jsonlite_1.7.2        
 [22] Rsamtools_2.6.0        ica_1.0-2              cluster_2.1.2         
 [25] png_0.1-7              uwot_0.1.10            ggforce_0.3.3         
 [28] shiny_1.7.1            sctransform_0.3.2      spatstat.sparse_2.0-0 
 [31] compiler_4.0.5         httr_1.4.2             assertthat_0.2.1      
 [34] Matrix_1.3-4           fastmap_1.1.0          lazyeval_0.2.2        
 [37] tweenr_1.0.2           later_1.3.0            htmltools_0.5.2       
 [40] tools_4.0.5            igraph_1.2.8           gtable_0.3.0          
 [43] glue_1.6.2             GenomeInfoDbData_1.2.4 RANN_2.6.1            
 [46] reshape2_1.4.4         fastmatch_1.1-3        Rcpp_1.0.7            
 [49] slam_0.1-48            scattermore_0.7        vctrs_0.3.8           
 [52] Biostrings_2.58.0      nlme_3.1-153           ggseqlogo_0.1         
 [55] lmtest_0.9-39          stringr_1.4.0          globals_0.14.0        
 [58] mime_0.12              miniUI_0.1.1.1         lifecycle_1.0.1       
 [61] irlba_2.3.3            goftest_1.2-3          future_1.21.0         
 [64] zlibbioc_1.36.0        MASS_7.3-54            zoo_1.8-9             
 [67] scales_1.1.1           spatstat.core_2.3-1    promises_1.2.0.1      
 [70] spatstat.utils_2.2-0   RColorBrewer_1.1-2     reticulate_1.22       
 [73] pbapply_1.5-0          gridExtra_2.3          rpart_4.1-15          
 [76] stringi_1.7.5          BiocParallel_1.24.1    rlang_0.4.12          
 [79] pkgconfig_2.0.3        matrixStats_0.62.0     bitops_1.0-7          
 [82] qlcMatrix_0.9.7        lattice_0.20-45        ROCR_1.0-11           
 [85] purrr_0.3.4            tensor_1.5             htmlwidgets_1.5.4     
 [88] cowplot_1.1.1          tidyselect_1.1.1       parallelly_1.28.1     
 [91] RcppAnnoy_0.0.19       plyr_1.8.6             magrittr_2.0.1        
 [94] R6_2.5.1               generics_0.1.1         DBI_1.1.1             
 [97] withr_2.4.2            mgcv_1.8-38            pillar_1.6.4          
[100] fitdistrplus_1.1-6     survival_3.2-13        abind_1.4-5           
[103] RCurl_1.98-1.5         tibble_3.1.6           future.apply_1.8.1    
[106] crayon_1.4.2           KernSmooth_2.23-20     utf8_1.2.2            
[109] spatstat.geom_2.3-0    plotly_4.10.0          grid_4.0.5            
[112] data.table_1.14.2      sparsesvd_0.2          digest_0.6.28         
[115] xtable_1.8-4           tidyr_1.1.4            httpuv_1.6.3          
[118] munsell_0.5.0          viridisLite_0.4.0
@pengxin2019 pengxin2019 added the bug Something isn't working label Nov 28, 2022
@timoast
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timoast commented Nov 28, 2022

This feature was added in Signac 1.7.0 (https://github.com/stuart-lab/signac/blob/master/NEWS.md#signac-170), please update to the latest release

@pengxin2019
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Hi Tim,
I just tried new version of Signac but i got another error.
Here is my code:

DefaultAssay(integrated) <- 'peaks'
Annotation(integrated)

ranges.show <- StringToGRanges("2-151108982-151113383")
p <- CoveragePlot(
  object = integrated,
  region = "2-151108982-151113383",#CSF1R
  extend.upstream = 25000,
  extend.downstream = 25000,
  show.bulk = TRUE,
  ranges = ranges.show,
  region.highlight = ranges.show,
  annotation="transcript"
)

Here is my error:

Error in cutmat[[1]] : this S4 class is not subsettable 

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

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

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

other attached packages:
[1] dplyr_1.0.7         patchwork_1.1.1     ggplot2_3.3.5      
[4] GenomeInfoDb_1.30.1 IRanges_2.28.0      S4Vectors_0.32.3   
[7] BiocGenerics_0.40.0 SeuratObject_4.0.4  Seurat_4.1.0       
[10] Signac_1.8.0       

loaded via a namespace (and not attached):
 [1] Rtsne_0.15             colorspace_2.0-2       deldir_1.0-5          
 [4] ellipsis_0.3.2         ggridges_0.5.3         XVector_0.34.0        
 [7] GenomicRanges_1.46.1   rstudioapi_0.13        spatstat.data_2.1-0   
[10] farver_2.1.0           leiden_0.3.9           listenv_0.8.0         
[13] ggrepel_0.9.1          fansi_0.5.0            codetools_0.2-18      
[16] splines_4.1.1          polyclip_1.10-0        RcppRoll_0.3.0        
[19] jsonlite_1.7.2         Rsamtools_2.10.0       ica_1.0-2             
[22] cluster_2.1.2          png_0.1-7              uwot_0.1.11           
[25] shiny_1.7.1            sctransform_0.3.3      spatstat.sparse_2.0-0 
[28] compiler_4.1.1         httr_1.4.2             assertthat_0.2.1      
[31] Matrix_1.3-4           fastmap_1.1.0          lazyeval_0.2.2        
[34] later_1.3.0            htmltools_0.5.2        tools_4.1.1           
[37] igraph_1.2.11          gtable_0.3.0           glue_1.4.2            
[40] GenomeInfoDbData_1.2.7 RANN_2.6.1             reshape2_1.4.4        
[43] fastmatch_1.1-3        Rcpp_1.0.7             scattermore_0.7       
[46] vctrs_0.3.8            Biostrings_2.62.0      nlme_3.1-152          
[49] lmtest_0.9-39          stringr_1.4.0          globals_0.14.0        
[52] mime_0.12              miniUI_0.1.1.1         lifecycle_1.0.1       
[55] irlba_2.3.5            goftest_1.2-3          future_1.22.1         
[58] zlibbioc_1.40.0        MASS_7.3-54            zoo_1.8-9             
[61] scales_1.1.1           spatstat.core_2.3-0    promises_1.2.0.1      
[64] spatstat.utils_2.2-0   parallel_4.1.1         RColorBrewer_1.1-2    
[67] reticulate_1.24        pbapply_1.5-0          gridExtra_2.3         
[70] rpart_4.1-15           stringi_1.7.5          BiocParallel_1.28.3   
[73] rlang_0.4.11           pkgconfig_2.0.3        matrixStats_0.61.0    
[76] bitops_1.0-7           lattice_0.20-44        ROCR_1.0-11           
[79] purrr_0.3.4            tensor_1.5             labeling_0.4.2        
[82] htmlwidgets_1.5.4      cowplot_1.1.1          tidyselect_1.1.1      
[85] parallelly_1.28.1      RcppAnnoy_0.0.19       plyr_1.8.6            
[88] magrittr_2.0.1         R6_2.5.1               generics_0.1.0        
[91] DBI_1.1.1              withr_2.4.2            mgcv_1.8-36           
[94] pillar_1.6.3           fitdistrplus_1.1-6     survival_3.2-11       
[97] abind_1.4-5            RCurl_1.98-1.5         tibble_3.1.5          
[100] future.apply_1.8.1     crayon_1.4.1           KernSmooth_2.23-20    
[103] utf8_1.2.2             spatstat.geom_2.3-0    plotly_4.10.0         
[106] grid_4.1.1             data.table_1.14.2      digest_0.6.28         
[109] xtable_1.8-4           tidyr_1.1.4            httpuv_1.6.3          
[112] munsell_0.5.0          viridisLite_0.4.0

@timoast
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timoast commented Nov 28, 2022

Can you show the output of traceback() after getting the error?

@pengxin2019
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traceback()
5: CoverageTrack(cutmat = cutmat[[1]], region = region, group.scale.factors = bulk.scale.factor,
scale.factor = scale.factor, window = window, ymax = ymax,
obj.groups = bulk.groups, downsample.rate = downsample.rate,
max.downsample = max.downsample)
4: SingleCoveragePlot(object = object, region = region[[x]], features = features,
expression.assay = expression.assay, expression.slot = expression.slot,
show.bulk = show.bulk, annotation = annotation, peaks = peaks,
peaks.group.by = peaks.group.by, ranges = ranges, ranges.group.by = ranges.group.by,
ranges.title = ranges.title, region.highlight = region.highlight,
assay = assay, split.assays = split.assays, assay.scale = assay.scale,
links = links, tile = tile, tile.size = tile.size, tile.cells = tile.cells,
bigwig = bigwig, bigwig.type = bigwig.type, bigwig.scale = bigwig.scale,
group.by = group.by, window = window, ymax = ymax, scale.factor = scale.factor,
extend.upstream = extend.upstream, extend.downstream = extend.downstream,
cells = cells, idents = idents, sep = sep, heights = heights,
max.downsample = max.downsample, downsample.rate = downsample.rate)
3: FUN(X[[i]], ...)
2: lapply(X = seq_along(region), FUN = function(x) {
SingleCoveragePlot(object = object, region = region[[x]],
features = features, expression.assay = expression.assay,
expression.slot = expression.slot, show.bulk = show.bulk,
annotation = annotation, peaks = peaks, peaks.group.by = peaks.group.by,
ranges = ranges, ranges.group.by = ranges.group.by, ranges.title = ranges.title,
region.highlight = region.highlight, assay = assay, split.assays = split.assays,
assay.scale = assay.scale, links = links, tile = tile,
tile.size = tile.size, tile.cells = tile.cells, bigwig = bigwig,
bigwig.type = bigwig.type, bigwig.scale = bigwig.scale,
group.by = group.by, window = window, ymax = ymax, scale.factor = scale.factor,
extend.upstream = extend.upstream, extend.downstream = extend.downstream,
cells = cells, idents = idents, sep = sep, heights = heights,
max.downsample = max.downsample, downsample.rate = downsample.rate)
})
1: CoveragePlot(object = integrated, region = "2-151108982-151113383",
extend.upstream = 25000, extend.downstream = 25000, show.bulk = TRUE,
ranges = ranges.show, region.highlight = ranges.show, annotation = "transcript")

timoast added a commit that referenced this issue Nov 28, 2022
@timoast
Fix show.bulk parameter; #1294
95bed38
@timoast
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timoast commented Nov 28, 2022

This should now be fixed on the the develop branch, see install instructions here: https://stuartlab.org/signac/articles/install.html#development-version

@timoast timoast closed this as completed Dec 1, 2022
@pengxin2019
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Hi Tim,
I took me a while to download it since I had permission issue on our hpc.

Unfortunately I still have an error. The integrated object is the same as what I have described.
here is my code:

ranges.show <- StringToGRanges("2-151108982-151113383")
p <- CoveragePlot(
 object = integrated,
 region = "2-151108982-151113383",#CSF1R
 extend.upstream = 25000,
 extend.downstream = 25000,
 show.bulk = TRUE,
 # ranges = ranges.show,
 region.highlight = ranges.show,
 annotation="transcript"
)

here is the error I got after script above was issued:
Error in cutmat[[1]] : this S4 class is not subsettable 

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

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

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

other attached packages:
 [1] dplyr_1.0.7         patchwork_1.1.1     ggplot2_3.3.5      
 [4] GenomeInfoDb_1.30.1 IRanges_2.28.0      S4Vectors_0.32.3   
 [7] BiocGenerics_0.40.0 SeuratObject_4.0.4  Seurat_4.1.0       
[10] Signac_1.8.0       

loaded via a namespace (and not attached):
  [1] fastmatch_1.1-3        plyr_1.8.6             igraph_1.2.11         
  [4] lazyeval_0.2.2         splines_4.1.1          BiocParallel_1.28.3   
  [7] listenv_0.8.0          scattermore_0.7        usethis_2.0.1         
 [10] digest_0.6.28          htmltools_0.5.2        fansi_0.5.0           
 [13] magrittr_2.0.1         memoise_2.0.0          tensor_1.5            
 [16] cluster_2.1.2          ROCR_1.0-11            remotes_2.4.1         
 [19] globals_0.14.0         Biostrings_2.62.0      matrixStats_0.61.0    
 [22] spatstat.sparse_2.0-0  prettyunits_1.1.1      colorspace_2.0-2      
 [25] ggrepel_0.9.1          callr_3.7.0            crayon_1.4.1          
 [28] RCurl_1.98-1.5         jsonlite_1.7.2         spatstat.data_2.1-0   
 [31] survival_3.2-11        zoo_1.8-9              glue_1.4.2            
 [34] polyclip_1.10-0        gtable_0.3.0           zlibbioc_1.40.0       
 [37] XVector_0.34.0         leiden_0.3.9           pkgbuild_1.2.0        
 [40] future.apply_1.8.1     abind_1.4-5            scales_1.1.1          
 [43] DBI_1.1.1              miniUI_0.1.1.1         Rcpp_1.0.7            
 [46] viridisLite_0.4.0      xtable_1.8-4           reticulate_1.24       
 [49] spatstat.core_2.3-0    htmlwidgets_1.5.4      httr_1.4.2            
 [52] RColorBrewer_1.1-2     ellipsis_0.3.2         ica_1.0-2             
 [55] farver_2.1.0           pkgconfig_2.0.3        uwot_0.1.11           
 [58] deldir_1.0-5           utf8_1.2.2             tidyselect_1.1.1      
 [61] rlang_0.4.11           reshape2_1.4.4         later_1.3.0           
 [64] munsell_0.5.0          tools_4.1.1            cachem_1.0.6          
 [67] cli_3.0.1              generics_0.1.0         devtools_2.4.2        
 [70] ggridges_0.5.3         stringr_1.4.0          fastmap_1.1.0         
 [73] goftest_1.2-3          processx_3.5.2         fs_1.5.0              
 [76] fitdistrplus_1.1-6     purrr_0.3.4            RANN_2.6.1            
 [79] pbapply_1.5-0          future_1.22.1          nlme_3.1-152          
 [82] mime_0.12              RcppRoll_0.3.0         compiler_4.1.1        
 [85] rstudioapi_0.13        plotly_4.10.0          curl_4.3.2            
 [88] png_0.1-7              testthat_3.1.0         spatstat.utils_2.2-0  
 [91] tibble_3.1.5           stringi_1.7.5          ps_1.6.0              
 [94] desc_1.4.0             lattice_0.20-44        Matrix_1.3-4          
 [97] vctrs_0.3.8            pillar_1.6.3           lifecycle_1.0.1       
[100] spatstat.geom_2.3-0    lmtest_0.9-39          RcppAnnoy_0.0.19      
[103] data.table_1.14.2      cowplot_1.1.1          bitops_1.0-7          
[106] irlba_2.3.5            httpuv_1.6.3           GenomicRanges_1.46.1  
[109] R6_2.5.1               promises_1.2.0.1       KernSmooth_2.23-20    
[112] gridExtra_2.3          parallelly_1.28.1      sessioninfo_1.1.1     
[115] codetools_0.2-18       MASS_7.3-54            assertthat_0.2.1      
[118] pkgload_1.2.2          rprojroot_2.0.2        withr_2.4.2           
[121] sctransform_0.3.3      Rsamtools_2.10.0       GenomeInfoDbData_1.2.7
[124] mgcv_1.8-36            parallel_4.1.1         grid_4.1.1            
[127] rpart_4.1-15           tidyr_1.1.4            Rtsne_0.15            
[130] shiny_1.7.1

Can you give me any further comments?

Thanks

@timoast
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timoast commented Dec 2, 2022

The session info shows that you still have the older version loaded, you'll need to update the package (see instructions linked above) and verify that the version that's loaded in your R session is 1.8.0.9003

@timoast timoast added this to the 1.9.0 milestone Dec 7, 2022
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Status: Q1 2023
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