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
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