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This script performs clustering analysis on gene expression data using the spatialGE package. It performs the STClust function from SpatialGE. The outputting .RDS object is a STList object for use in downstream Spatial GE analysis / visualization.
- Authors: Edwin Huang, Aditya Kakarla
- Categories: Spatial transcriptomics
- Source Repo: Link: https://github.com/FridleyLab/spatialGE
- Contact: Link: https://groups.google.com/u/1/g/genepattern-help
- Programming Language: R
| Info | Type |
|---|---|
input.RDS |
Required |
CellComposite.zip |
Optional |
| Info | Type |
|---|---|
spatialGE_STclustered.rds |
Required |
| Parameter | Name | Description | Default Value | Type |
|---|---|---|---|---|
--e (--stlist) |
-e |
A required option that specifies a STList object in .RDS file format to cluster on. | None |
str |
--w (--ws) |
-w |
An optional parameter that sets the weight to be applied to spatial distances. The default value is 0.025. | 0.025 |
float |
--d (--dist_metric) |
-d |
An optional parameter that specifies the distance metric to be used. The default value is 'euclidean'. | 'euclidean' |
str |
--l (--linkage) |
-l |
An optional parameter that specifies the linkage method to be used for hierarchical clustering. The default value is 'ward.D2'. | 'ward.D2' |
str |
--k (--ks) |
-k |
An optional parameter that specifies the range of k values to assess. The default value is 'dtc'. | 2000 |
int |
--t (--topgenes) |
-t |
An optional integer parameter that sets the number of genes with highest spot-to-spot expression variation. The default value is 2000. | 2000 |
int |
--s (--deepSplit) |
-s |
An optional logical parameter that controls cluster resolution. The default value is FALSE. | FALSE |
bool |
--p (--plot) |
-p |
An optional logical parameter that enables or disables plotting intermediate results. The default value is FALSE. | FALSE |
bool |
--o (--output) |
-o |
An optional character parameter that specifies the path to save the output STList object. The default value is 'spatialGE_STclustered.rds'. | 'spatialGE_STclustered.rds' |
str |
--keep_fovs |
--keep_fovs |
An optional character parameter that specifies a comma-separated list of FOVs (Focus Organizations) to keep. If not specified, no filtering is done. | None |
str |
--spot_minreads |
--spot_minreads |
An optional integer parameter that sets the minimum number of reads per spot. The default value is 20. | 20 |
int |
--rm_genes_expr |
--rm_genes_expr |
An optional character parameter that specifies a regular expression to filter out genes. The default value is '^NegPrb'. | ^NegPrb |
str |
--rm_tissue |
--rm_tissue |
An optional character parameter that specifies a comma-separated list of tissues to remove. If not specified, no filtering is done. | None |
str |