Workflow clustering

[KarinSchork]

No description provided.

[Copilot]

Pull request overview

This pull request introduces a new workflow for clustering proteins based on similar patterns across samples, producing heatmaps and line plots. The changes refactor the existing clustering functionality into modular, reusable components and provide a high-level workflow function for users.

Changes:

• Added new workflow_clustering() function that provides a complete workflow for protein clustering analysis
• Refactored the monolithic Clustering_heatmap_lineplots() function into three separate, modular functions: clustering(), getClusterInfos(), and Lineplots()
• Updated documentation for better clarity and added the id parameter to PCA-related functions

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
R/WIP_workflow_clustering_heatmap.R	New workflow function that orchestrates the clustering analysis
R/WIP_Clustering_Heatmap_Lineplots.R	Refactored clustering logic into modular functions
man/workflow_clustering.Rd	Documentation for the new workflow function
man/clustering.Rd	Documentation for the clustering function
man/getClusterInfos.Rd	Documentation for cluster information extraction
man/Lineplots.Rd	Documentation for lineplot generation
man/Clustering_heatmap_lineplots.Rd	Removed documentation for deprecated function
man/workflow_ttest.Rd	Improved suffix parameter description
R/workflow_ttest.R	Improved suffix parameter description
man/filter_PCA_data.Rd	Added new id parameter documentation
man/PCA_Plot.Rd	Added new id parameter documentation
NAMESPACE	Updated exports to reflect new and removed functions
DESCRIPTION	Version bump from 0.1.1 to 0.2.0

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[Copilot]

Inconsistent variable usage. The variable 'nr_clusters' is used here, but it may still be NULL at this point. You should use 'clust$nr_clusters' instead to ensure the correct value is used in the filename.

[KarinSchork]

@copilot open a new pull request to apply changes based on this feedback

[Copilot]

Inconsistent variable usage. The variable 'nr_clusters' is used here, but it may still be NULL at this point. You should use 'clust$nr_clusters' instead to ensure the correct value is used in the filename.

[Copilot]

Inconsistent variable usage. The variable 'nr_clusters' is used here, but it may still be NULL at this point. You should use 'clust$nr_clusters' instead to ensure the correct value is used in the filename.

Suggested change

	row_split = nr_clusters,
	row_gap = grid::unit(5, "mm"),
	...)
	grDevices::png(paste0(output_path, "/heatmap", suffix, "_", nr_clusters, ".png"),
	height = plot_height_heatmap,
	width = plot_width_heatmap, units = "cm", res = plot_dpi)
	graphics::plot(ht)
	grDevices::dev.off()
	clusterInfo <- getClusterInfos(heatmap = ht, nr_clusters = nr_clusters, D = dataPrep$D, id = dataPrep$id)
	openxlsx::write.xlsx(clusterInfo, paste0(output_path, "/cluster_table", suffix, "_", nr_clusters, ".xlsx"))
	D_zscore <- cbind(ht@matrix, cluster = clusterInfo$cluster)
	lineplots <- Lineplots(D_zscore = D_zscore, cluster_colours = clust$cluster_colours)
	grDevices::pdf(paste0(output_path, "/Lineplots", suffix, "_", nr_clusters, ".pdf"),
	row_split = clust$nr_clusters,
	row_gap = grid::unit(5, "mm"),
	...)
	grDevices::png(paste0(output_path, "/heatmap", suffix, "_", clust$nr_clusters, ".png"),
	height = plot_height_heatmap,
	width = plot_width_heatmap, units = "cm", res = plot_dpi)
	graphics::plot(ht)
	grDevices::dev.off()
	clusterInfo <- getClusterInfos(heatmap = ht, nr_clusters = clust$nr_clusters, D = dataPrep$D, id = dataPrep$id)
	openxlsx::write.xlsx(clusterInfo, paste0(output_path, "/cluster_table", suffix, "_", clust$nr_clusters, ".xlsx"))
	D_zscore <- cbind(ht@matrix, cluster = clusterInfo$cluster)
	lineplots <- Lineplots(D_zscore = D_zscore, cluster_colours = clust$cluster_colours)
	grDevices::pdf(paste0(output_path, "/Lineplots", suffix, "_", clust$nr_clusters, ".pdf"),

[Copilot]

@KarinSchork I've opened a new pull request, #60, to work on those changes. Once the pull request is ready, I'll request review from you.