FragmentHistogram Error: in combine_vars(): ! Faceting variables must have at least one value.

[xiaoxiaoh16]

Hi @timoast, thanks fo the nice package, I have the result of Cellrager-atac output (filtered_peak_bc_matrix.h5, fragments.tsv.gz
fragments.tsv.gz.tbi, singlecell.csv) as the input of Signac , I have some issues when I try to use FragmentHistogram function to plot. The error information and packages verison as following.

1. packages verison:

packageVersion("Signac")
[1] '1.11.0'
packageVersion("GenomeInfoDb")
[1] '1.36.4'
packageVersion("Seurat")
[1] '4.4.0'
packageVersion("GenomicFeatures")
[1] '1.52.2'
packageVersion("ggplot2")
[1] '3.4.4'

2. Error message:

FragmentHistogram(object = pbmc, group.by = 'nucleosome_group')
Error in combine_vars():
! Faceting variables must have at least one value
Run rlang::last_trace() to see where the error occurred.

rlang::last_trace()
<error/rlang_error>
Error in combine_vars():
! Faceting variables must have at least one value

---

Backtrace:
▆

1. ├─base (local) <fn>(x)
2. └─ggplot2:::print.ggplot(x)
3. ├─ggplot2::ggplot_build(x)
4. └─ggplot2:::ggplot_build.ggplot(x)

5. └─layout$setup(data, plot$data, plot$plot_env)
   

6.   └─ggplot2 (local) setup(..., self = self)
   

7.     └─self$facet$compute_layout(data, self$facet_params)
   

8.       └─ggplot2 (local) compute_layout(..., self = self)
   

9.         └─ggplot2::combine_vars(data, params$plot_env, vars, drop = params$drop)
   

Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.

3. Other information:

table(pbmc$nucleosome_group)

NS < 4 NS > 4
3811 67

head(pbmc$nucleosome_signal)
AAACGAAAGTAATCAG-1 AAACGAACACGCTGTG-1 AAACGAATCCTGGGAC-1 AAACGAATCGGGAAAC-1
0.9176285 0.6792104 0.5595331 0.7097404
AAACTCGAGAAAGCAG-1 AAACTCGAGAATAGTC-1
0.9242579 10.2473118

Please let me know if you need other information.
Thank you in advance!

[timoast]

Try increasing the size of the region parameter, probably there were no fragments found in the default region for the cells with NS > 4