Merge pull request #1 from genepattern/main

Sync main and develop
genepattern · Dec 18, 2024 · 566cb2f · 566cb2f
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diff --git a/docs/v1/index.md b/docs/v1/index.md
@@ -1,17 +1,14 @@
 # spatialGE.STenrich (v1)
 
-The `spatialGE.Preprocessing` module is part of the spatialGE package. It detects genes showing spatial expression patterns (e.g., hotspots) and tests if spots/cells with a high average expression of a gene set show evidence of spatial aggregation.
+The `spatialGE.STenrich` module is part of the spatialGE package. It detects genes showing spatial expression patterns (e.g., hotspots) and tests if spots/cells with a high average expression of a gene set show evidence of spatial aggregation.
 
 ## Module Details
 
 - **Authors:** Thorin Tabor, Ted Liefeld, Edwin Huang, Michael Reich; UCSD - Mesirov Lab
 - **Categories:** spatial transcriptomics
 - **Source repository:** [spatialGE.Preprocessing on GitHub](https://github.com/genepattern/spatialGE.STenrich)
 - **Contact**: [GenePattern Help Forum](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!forum/genepattern-help)
-
-**Contact**: [Forum Link](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!forum/genepattern-help)
-
-**Algorithm Version**: [spatialGE 1.2.0](https://fridleylab.github.io/spatialGE/)
+- **Algorithm Version**: [spatialGE 1.2.0](https://fridleylab.github.io/spatialGE/)
 
 ## Summary
 
@@ -31,17 +28,17 @@ Ospina, O. E., Wilson C. M., Soupir, A. C., Berglund, A. Smalley, I., Tsai, K. Y
 ## Parameters
 <!-- short description of the module parameters and their default values, as well as whether they are required -->
 
-| Name                 | Description                                                                                                                                                                              | Default Value |
-----------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|
-| input file *         | Normalized spatial transcriptomics data coming from the spatialGE.Preprocessing module.                                                                                                  |
-| gene sets database * | Select a gene set database to test for spatial enrichment. Upload a gene set if your gene set is not listed as a choice from MSigDB.                                                     |               |
-| permutations *       | The number of permutations to estimate the null distribution (no-spatial pattern). The more permutations, the longer STenrich takes to complete, but p-values may be more accurate.      | 100           |
-| random seed *        | A seed number to replicate results. It is advisable to run STenrich with different seed values to check for consistency. Different seed values could yield slightly different p-values. | 12345         |
-| minumum spots * | The minimum number of high expression ROIs/spots/cells required for a gene set to be tested. If a sample has less than this number of high expression ROIs/spots/cells, the gene set is not tested in that sample. | 5 |
-| minimum genes * | The minimum number of genes of a set required to be present in a sample, for that gene set to be tested in that sample. If a sample has less genes of a set than this number, the gene set is ignored in that sample. | 5 |
-| standard deviations * | The number of standard deviations to define the high expression threshold. If an ROI/spot/cell has average gene set expression larger than the entire sample average plus this many standard deviations, it will be considered a high-expression ROI/spot/cell. | 1.0 |
-| filter p values * | Plot only gene sets whose multiple test adjusted p-value is less than this threshold. | 0.05 |
-| filter gene proportion * | Plot only gene sets where the proportional number genes in the set present in the field of view equals or exceeds this threshold. | 0.3 |
+| Name                     | Description                                                                                                                                                                                                                                                     | Default Value |
+|--------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|
+| input file *             | Normalized spatial transcriptomics data coming from the spatialGE.Preprocessing module.                                                                                                                                                                         |               |
+| gene sets database *     | Select a gene set database to test for spatial enrichment. Upload a gene set if your gene set is not listed as a choice from MSigDB.                                                                                                                            |               |
+| permutations *           | The number of permutations to estimate the null distribution (no-spatial pattern). The more permutations, the longer STenrich takes to complete, but p-values may be more accurate.                                                                             | 100           |
+| random seed *            | A seed number to replicate results. It is advisable to run STenrich with different seed values to check for consistency. Different seed values could yield slightly different p-values.                                                                         | 12345         |
+| minumum spots *          | The minimum number of high expression ROIs/spots/cells required for a gene set to be tested. If a sample has less than this number of high expression ROIs/spots/cells, the gene set is not tested in that sample.                                              | 5             |
+| minimum genes *          | The minimum number of genes of a set required to be present in a sample, for that gene set to be tested in that sample. If a sample has less genes of a set than this number, the gene set is ignored in that sample.                                           | 5             |
+| standard deviations *    | The number of standard deviations to define the high expression threshold. If an ROI/spot/cell has average gene set expression larger than the entire sample average plus this many standard deviations, it will be considered a high-expression ROI/spot/cell. | 1.0           |
+| filter p values *        | Plot only gene sets whose multiple test adjusted p-value is less than this threshold.                                                                                                                                                                           | 0.05          |
+| filter gene proportion * | Plot only gene sets where the proportional number genes in the set present in the field of view equals or exceeds this threshold.                                                                                                                               | 0.3           |
 
 \*  required
 
@@ -72,6 +69,6 @@ Requires the [genepattern/spatialge-stenrich:0.4 Docker image](https://hub.docke
 
 ## Version Comments
 
-| Version | Release Date  | Description                       |
-----------|---------------|-----------------------------------|
-| 1 | June 28, 2024 | Initial version |
+| Version | Release Date  | Description     |
+|---------|---------------|-----------------|
+| 1       | June 28, 2024 | Initial version |
diff --git a/manifest b/manifest
@@ -147,4 +147,4 @@ quality=development
 taskDoc=
 taskType=spatial transcriptomics
 userid=tabor
-version=Initial development release
+version=Write stlist rds to disk
diff --git a/src/wrapper.R b/src/wrapper.R
@@ -71,3 +71,5 @@ ggsave(
   dpi = 300,
   limitsize = TRUE
 )
+
+saveRDS(stenrich_out, file='enrich_stlist.rds')