Manage scanpy plots #23
Open
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
Deconstruct nextflow script
Test nsforest module
Add preprocessing option
Fix result directory path
ralatsdc
commented
Jan 17, 2025
| @@ -0,0 +1,455 @@ | |||
| #!/usr/bin/env python | |||
There was a problem hiding this comment.
This is a script I use for demonstrating how to run NSForest using Nextflow
ralatsdc
commented
Jan 17, 2025
| markers_dict = dict(zip(df_results["clusterName"], df_results["NSForest_markers"])) | ||
| on_target_ratio = calculate_fraction.markers_onTarget(adata, cluster_header, markers_dict, medians_header, save_supplementary = save_supplementary, output_folder = output_folder, outputfilename_prefix = outputfilename_prefix) | ||
| df_results = df_results.merge(on_target_ratio, on = "clusterName", how = "left") | ||
| if not df_results.empty: |
There was a problem hiding this comment.
Encountered an error when df_results as empty
ralatsdc
commented
Jan 17, 2025
| @@ -45,7 +45,7 @@ def scatter_w_clusterSize(df, col, save = False, output_folder = "", outputfilen | |||
| col: str | |||
| Column in `df` to plot against "clusterSize". | |||
| save: bool (default: False) | |||
| Whether to save html file. | |||
| Whether to save plot as an SVG file. | |||
There was a problem hiding this comment.
I need SVG plots in order to make the plots interactive in the user interface
ralatsdc
commented
Jan 17, 2025
| @@ -64,37 +64,39 @@ def scatter_w_clusterSize(df, col, save = False, output_folder = "", outputfilen | |||
| fig.write_html(filename) | |||
| return fig | |||
|
|
|||
| def dotplot(adata, markers, cluster_header, gene_symbols = None, dendrogram = True, save = False, output_folder = "", outputfilename_suffix = ""): | |||
| def dotplot(adata, markers, cluster_header, gene_symbols = None, dendrogram = True, save = False, show = False, output_folder = "", outputfilename_suffix = ""): | |||
There was a problem hiding this comment.
The plots of interest use scanpy, which allows setting of save and show separately. Show is helpful when interactive, but problematic when running non-interactively, for example, in Nextflow. Allowing save to be optional just seems sensible and consistent.
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.
No description provided.