CoveragePlot error on ATAC data

[Bojung2540]

Hello, @timoast .
I have doubts about using the CoveragePlot() function of the Signac package version 1.8.0.

The code that I used is as shown here.

CoveragePlot(object = coembed.atac,
region = rownames(da_peaks_A)[1],
extend.upstream = 1000,
extend.downstream = 1000)

Where rownames(da_peaks_A)[1] = "Chr1-12933056-12940246"

And I get the error as follows:

Error in `colnames<-`(`*tmp*`, value = start(x = region):end(x = region)) :
attempt to set 'colnames' on an object with less than two dimensions

Here is the traceback:

6. stop("attempt to set 'colnames' on an object with less than two dimensions")
5. `colnames<-`(`*tmp*`, value = start(x = region):end(x = region))
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, ...
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, ...
1. CoveragePlot(object = coembed.atac, region = rownames(da_peaks_A)[1],
extend.upstream = 1000, extend.downstream = 1000)

Here is the assay that I use:

coembed.atac[['ATAC']]

ChromatinAssay data with 22749 features for 1004 cells
Variable features: 0
Genome:
Annotation present: TRUE
Motifs present: TRUE
Fragment files: 0

I'm not sure if the error that's occurring is a result of this ChromatinAssay lacking a fragment file.

I apologize if this question has been raised previously.

Thank you.

[timoast]

I'm not sure if the error that's occurring is a result of this ChromatinAssay lacking a fragment file.

Yes, a fragment file is required for making these plots. We'll add a more informative error message for this case.

[Bojung2540]

Thank you very much.