Adding TSCAN Trajectory function to the package - #91
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Pull request overview
Adds a new TSCAN-based trajectory analysis entry point to SCWorkflow (ported from the NIDAP 1.0 beta template) and introduces minimal tests around basic argument validation and smoke-running.
Changes:
- Introduces
Trajectory_CellTypes()implementing a TSCAN/TrajectoryUtils pseudotime workflow with plotting side effects. - Adds a new testthat file covering missing cluster column, invalid argument types, and a minimal “runs without error” case.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.
| File | Description |
|---|---|
| R/Trajectory_CellTypes_v12.R | Adds the new TSCAN trajectory function plus internal helpers. |
| tests/testthat/test-Trajectory_CellTypes_v12.R | Adds tests for basic validation and a minimal run path. |
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| required_packages <- c( | ||
| "Seurat", "scater", "scran", "scuttle", "TrajectoryUtils", "TSCAN", | ||
| "ggplot2", "gridExtra", "mclust", | ||
| "SingleCellExperiment", "SummarizedExperiment" | ||
| ) | ||
| ensure_namespace(required_packages) |
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| #' @export | ||
| Trajectory_CellTypes <- function(Seurat_Object, | ||
| MetaData, | ||
| Clusters_to_Use, | ||
| Custom_Gene_List = NULL) { |
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| scater::plotHeatmap( | ||
| sce[, on_first_path], | ||
| order_columns_by = "Pseudotime", | ||
| colour_columns_by = "label", | ||
| features = head(top_up, 50), | ||
| center = TRUE, | ||
| main = "Expression of the top 50 genes that increase with pseudotime" | ||
| ) | ||
| scater::plotHeatmap( | ||
| sce[, on_first_path], | ||
| order_columns_by = "Pseudotime", | ||
| colour_columns_by = "label", | ||
| features = head(top_down, 50), | ||
| center = TRUE, | ||
| main = "Expression of the top 50 genes that decrease with pseudotime" |
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Leaving this "AS IS" for compatibility purposes, but worth looking into
Fixing R_USER_CACHE_DIR in read-only scenario Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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I ran tests locally and they passed the TSCAN tests |
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Introducing TSCAN Trajectory function from NIDAP 1.0 beta template into SCWorkflow package for compatibility with existing analyses