CoveragePlot: not able to visualize genes corresponding to the peaks in the genomic regions

[pengxin2019]

Hi Tim,
I am working on non-human scATAC datasets following your pipeline here:
https://satijalab.org/signac/articles/pbmc_vignette.html

But I have an error in the CoveragePlot which is at the bottom of your pipeline.

#da_peaks$region[167]
#[1] "49998118-50000003"

head(Annotation(integrated))

# GRanges object with 6 ranges and 8 metadata columns:
#   GRanges object with 6 ranges and 8 metadata columns:
#   seqnames        ranges strand |            gene_id
# <Rle>     <IRanges>  <Rle> |        <character>
#   ENSSSCG00000037372        1    3472-18696      - | ENSSSCG00000037372
# ENSSSCG00000027257        1   23368-40113      + | ENSSSCG00000027257
# ENSSSCG00000029697        1  96218-186785      - | ENSSSCG00000029697
# ENSSSCG00000027274        1 112763-113499      - | ENSSSCG00000027274
# ENSSSCG00000027726        1 198992-211342      + | ENSSSCG00000027726
# ENSSSCG00000033475        1 352196-356072      + | ENSSSCG00000033475
# gene_name   gene_biotype seq_coord_system
# <character>    <character>      <character>
#   ENSSSCG00000037372         TBP protein_coding       chromosome
# ENSSSCG00000027257       PSMB1 protein_coding       chromosome
# ENSSSCG00000029697     FAM120B protein_coding       chromosome
# ENSSSCG00000027274             protein_coding       chromosome
# ENSSSCG00000027726        DLL1 protein_coding       chromosome
# ENSSSCG00000033475                    lincRNA       chromosome
# description      gene_id_version      symbol
# <character>          <character> <character>
#   ENSSSCG00000037372 TATA-box binding pro.. ENSSSCG00000037372.1         TBP
# ENSSSCG00000027257 proteasome subunit b.. ENSSSCG00000027257.2       PSMB1
# ENSSSCG00000029697 family with sequence.. ENSSSCG00000029697.2     FAM120B
# ENSSSCG00000027274                   NULL ENSSSCG00000027274.2            
# ENSSSCG00000027726 delta like canonical.. ENSSSCG00000027726.2        DLL1
# ENSSSCG00000033475                   NULL ENSSSCG00000033475.1            
# entrezid
# <list>
#   ENSSSCG00000037372 110259740
# ENSSSCG00000027257 100621969
# ENSSSCG00000029697 100620583
# ENSSSCG00000027274      <NA>
#   ENSSSCG00000027726 100620481
# ENSSSCG00000033475      <NA>
#   -------
#   seqinfo: 352 sequences from Sscrofa11.1 genome


CoveragePlot(
  object = integrated,
  region = da_peaks$region[167], #CD79A
  extend.upstream = 40000,
  extend.downstream = 20000
)

#the error look like this:
Error in annotation[annotation$type == "body", ] : 
  incorrect number of dimensions

Does this error result from that there is no information on whether the region on each row correspond to an exon or intron?
For example, in the "seq_coord_system" of the head(Annotation(integrated)). it only says "chromosome" rather saying "intron" or "exon"

If I set up the annotation to be FALSE:

CoveragePlot(
  object = integrated,
  region = da_peaks$region[167], #CD79A
  extend.upstream = 40000,
  extend.downstream = 20000
  annotation = FALSE
)

The plot would look like below which is not what I want. I hope I can visualize the genes

Can you give me some suggestions?

Thanks

[timoast]

For troubleshooting errors, please open an issue instead. Please also include the full code you're running and the output of sessionInfo()