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remove stabmap section of vignette
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Max Woollard authored and Max Woollard committed Aug 14, 2024
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4 changes: 3 additions & 1 deletion man/wSIR.Rd

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13 changes: 3 additions & 10 deletions vignettes/wSIR_vignette.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -393,14 +393,7 @@ use include spatial alignment of single-cell and spatial gene expression data
via [Tangram](https://www.nature.com/articles/s41592-021-01264-7), using the
wSIR scores as the input rather than the (unreduced) gene expression matrix.

<<<<<<< HEAD
An example of a very simple application is using the wSIR scores as an input to a KNN cell type classification algorithm. This is demonstrated below, using the 'knn' function from 'class' package.
=======
An example of a simple application is using the wSIR scores as an input to a
KNN cell type classification algorithm from the
[StabMap](https://bioconductor.org/packages/devel/bioc/html/StabMap.html)
package. This is demonstrated below.
>>>>>>> 153f42b2334a02ea08c589e0c07ceca55df1b2c3

```{r}
samples12_cell_types = append(sample1_cell_types, sample2_cell_types)
Expand All @@ -410,11 +403,11 @@ knn_classification_object = knn(train = wsir_obj_samples12$scores,
cl = samples12_cell_types,
k = 10)
head(knn_classification_object)
tail(knn_classification_object)
```

In the above code, we use the wSIR scores as input for StabMap's KNN-based
cell type classification tool. We print the tail of the prediction dataframe,
In the above code, we use the wSIR scores as input for a simple KNN-based
cell type classification tool. We print the tail of the prediction vector,
demonstrating how we can use the wSIR-based low-dimensional gene expression
data from a new sample as a step in a realistic analysis pipeline.

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