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add rworkflows as suggest
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bschilder committed Oct 21, 2023
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -50,6 +50,7 @@ Imports:
dplyr,
pals
Suggests:
rworkflows,
markdown,
rmarkdown,
magick,
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10 changes: 9 additions & 1 deletion vignettes/echoplot.Rmd
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Expand Up @@ -174,8 +174,15 @@ methods::show(trk_plot.xgr)
* Note that Roadmap queries requires `tabix` to be installed on your machine, or within a conda environment (`conda_env = "echoR"`).
* Parallelizing these queries across multiple thredas speeds up this process (`nThread=<n_cores_available>`), as does reusing previously stored data which is automatically saved to the locus-specific subfolder (`<dataset_type>/<dataset_name>/<locus>/annotations/Roadmap.ChromatinMarks_CellTypes.RDS`).


*NOTE*: Querying remote genomic data sources (e.g. Roadmap bigwigs) is not currently
supported on Windows due to known bugs in
[`rtracklayer`](https://github.com/lawremi/rtracklayer/issues).

```{r trk_plot.roadmap, attr.output='style="max-height: 200px;"'}
trk_plot.roadmap <- echoplot::plot_locus(dat=dat,
if(.Platform!="windows"){
trk_plot.roadmap <- echoplot::plot_locus(dat=dat,
LD_matrix=LD_matrix,
LD_reference=LD_reference,
locus_dir=locus_dir,
Expand All @@ -186,6 +193,7 @@ trk_plot.roadmap <- echoplot::plot_locus(dat=dat,
save_plot=FALSE,
show_plot=show_plot,
zoom="5x")
}
```

```{r}
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