IdoBar
commented
1 month ago Just a quick update, when I specify heatmap=FALSE, it generates a plot, but it is empty with no traces.
plot_gene(mbr, "EKO05_006932", heatmap = FALSE, spaghetti = TRUE)Closed IdoBar closed 1 month ago
IdoBar
commented
1 month ago Just a quick update, when I specify heatmap=FALSE, it generates a plot, but it is empty with no traces.
plot_gene(mbr, "EKO05_006932", heatmap = FALSE, spaghetti = TRUE)
Shians
commented
1 month ago Hmm that's not an error I've seen before, when you get an error, are you able to get any information from traceback(). The only unusual thing I can see is using a very cutting edge version of ggplot2, but that really shouldn't cause this problem.
IdoBar
commented
1 month ago It seems that there are issues with patchwork and recent versions of ggplot2, I actually reverted back to v3.4.4 (based on this discussion) and updated pathcwork, which solved some problem with patchwork, but the plotting functions in NanoMethViz still don't work.
This is my last_trace() output:
Error in `combine_vars()`:
! Faceting variables must have at least one value
---
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. └─patchwork:::print.patchwork(x)
3. └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
4. └─base::lapply(x$plots, plot_table, guides = guides)
5. ├─patchwork (local) FUN(X[[i]], ...)
6. └─patchwork:::plot_table.ggplot(X[[i]], ...)
7. └─ggplot2::ggplotGrob(x)
8. ├─ggplot2::ggplot_gtable(ggplot_build(x))
9. │ └─ggplot2:::attach_plot_env(data$plot$plot_env)
10. │ └─base::options(ggplot2_plot_env = env)
11. ├─ggplot2::ggplot_build(x)
12. └─ggplot2:::ggplot_build.ggplot(x)
13. └─layout$setup(data, plot$data, plot$plot_env)
14. └─ggplot2 (local) setup(..., self = self)
15. └─self$facet$compute_layout(data, self$facet_params)
16. └─ggplot2 (local) compute_layout(..., self = self)
17. └─ggplot2::combine_vars(data, params$plot_env, vars, drop = params$drop)Can you recommend versions of patchwork and ggplot2 that you are using so I could try?
IdoBar
commented
1 month ago I have an update - after updating both ggplot2 and patchwork and changing the sample names to not include dashes (following this thread on Bioconductor) I can get the plot if I turn off the heatmap.
plot_gene(mbr, "EKO05_006932", heatmap = FALSE, spaghetti = FALSE)nmr <- load_example_nanomethresult()
plot_gene(nmr, "Peg3", heatmap = FALSE)With heatmap=TRUE I still get the error:
> plot_gene(nmr, "Peg3")
Error in self$get_transformation() : attempt to apply non-functionI am currently working with ggplot2_3.5.1 and patchwork_1.3.0.
IdoBar
commented
1 month ago I am currently working with ggplot2_3.5.1 and patchwork_1.3.0.
Thanks, it's working with these versions.
Hi, I'm very excited about this package, but I'm unable to generate methylation plots. I created an
mbrobject from BAM files generated bydorado(usingsup,5mCG_5hmCG,6mAmodels). The data seems to be loaded correctly and I can see the methylation probabilities:But when trying to plot them, I'm getting the following error message:
When trying to use the provided
nmrexample, I'm getting the following error:This is my session info:
Any help would be appreciated!
Thanks, Ido