Dependency cleanup and setting up actions #55
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This was
linked to
issues
Mar 17, 2024
Closed
Closed
Closed
R/fancy_alignment_plot.R
Outdated
| @@ -25,7 +25,7 @@ | |||
| #' @return A plot as a ggplot object (grob). | |||
| #' | |||
| #' @rawNamespace import(data.table, except = c("last", "first", "between", "transpose", "melt", "dcast")) | |||
| #' @import ggplot2 cowplot dplyr | |||
| #' @import ggplot2 GAMBLR.helpers dplyr | |||
There was a problem hiding this comment.
> fancy_alignment_plot(these_sample_ids = my_samples)
Using bundled metadata from GAMBLR.data
Using the bundled collated results in GAMBLR.data...
Using the bundled metadata in GAMBLR.data...
QC Metric successfully retreived for 89 samples out of a total of samples in input sample table.
Error in melt(., id.var = "sample_id") : could not find function "melt"
Need to add @importFrom reshape2 melt.
There was a problem hiding this comment.
One of the issues this PR addresses is dependency burden, so instead of adding this package I re-implemented this with a superior pivot_longer function.
R/prettyForestPlot.R
Outdated
|
|
||
| arranged_plot = cowplot::plot_grid(plot_grid(NULL, legend, NULL, nrow = 1), plots, nrow = 2, rel_heights = c(0.1, 1)) | ||
| arranged_plot = ggarrange( | ||
| replica$forest, |
There was a problem hiding this comment.
metadata = GAMBLR.results::get_gambl_metadata()
this_meta = dplyr::filter(metadata, pairing_status == "matched")
this_meta = dplyr::filter(this_meta, pathology %in% c("FL", "DLBCL"))
maf = get_ssm_by_sample(these_samples_metadata = this_meta)
prettyForestPlot(maf = maf,
metadata = this_meta,
genes = c("ATP6V1B2",
"EZH2",
"TNFRSF14",
"RRAGC"),
comparison_column = "pathology",
comparison_values = c("DLBCL",
"FL"),
separate_hotspots = FALSE,
comparison_name = "FL vs DLBCL")
FONT: 20 POINT: 16.6666666666667 3
Error in ggarrange(replica$forest, replica$bar, widths = c(1, 0.6), common.legend = TRUE, :
object 'replica' not found
R/fancy_ideogram.R
Outdated
There was a problem hiding this comment.
This function calls GAMBLR.utils::gene_to_region using the wrong parameter genome_build. Could you change it to projection.
vladimirsouza
approved these changes
Mar 19, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR ensures the viz package passes devtools check, brings documentation in place, reduces dependencies burden, and sets up the githbub actions build check similar to other packages. The issues directly addressed here are:
Pull Request Checklists
Important: When opening a pull request, keep only the applicable checklist and delete all other sections.
Checklist for all PRs
Required
<package>::function()syntax.@importsection of the documentation