Hi I have a GAlignments Object from scanning 1000-1100 of chromosome x of a bam file

GAlignments object with 46 alignments and 5 metadata columns:
       seqnames strand       cigar    qwidth     start       end     width     njunc   |    rname
          <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> <integer>   | <factor>
   [1]     seq1      +         35M        35       970      1004        35         0   |     seq1
   [2]     seq1      +         35M        35       971      1005        35         0   |     seq1

Running coverage() on the object I get an RleList that looks something like this

RleList of length 2
$seq1
integer-Rle of length 1575 with 52 runs
  Lengths: 969   1   1   1   1   1   1   5   1   1   1 ...   1   1   1   1   2   1   1   3   1 531
  Values :   0   1   2   3   4   5   6   7  10  12  14 ...  15  12  11  10   8   7   5   4   2   0

$seq2
integer-Rle of length 1584 with 1 run
  Lengths: 1584
  Values :    0

I want to graph the coverage data (of the chunk I scanned) with ggbio or ggplot2 but I'm not sure exactly what the coverage result represents. Is there a way to get a graph with chromosome location I've scanned on the x axis and read coverage on the y with this? Or are the results usually graphed a different way?

Thanks

Hello, thanks for your help. I haven't been able to get stat_coverage to fully graph the data

I can convert my GAlignments Object to a GRangesList but not a GRanges

bamranges<-as(bamaligns,"GRanges")
Error in `elementMetadata<-`(x, ..., value = value) : 
  names of metadata columns cannot be one of  "seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", "width", "element"

bamranges

GRangesList object of length 46:
[[1]] 
GRanges object with 1 range and 0 metadata columns:
      seqnames      ranges strand
         <Rle>   <IRanges>  <Rle>
  [1]     seq1 [970, 1004]      +

[[2]] 
GRanges object with 1 range and 0 metadata columns:
      seqnames      ranges strand
  [1]     seq1 [971, 1005]      +

when I attempt to use the GRangesList in stat_coverage I also get an error.

> ggplot()+stat_coverage(bamranges)
Error in `elementMetadata<-`(`*tmp*`, value = <S4 object of class "DataFrame">) : 
  names of metadata columns cannot be one of  "seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "start", "end", "width", "element"

I can graph one element of the GRangesList but that is not particularly useful

> ggplot()+stat_coverage(bamranges[[1]])