Merge branch 'devel' of https://github.com/SydneyBioX/spicyR into devel

vignettes/spicyR.Rmd

@@ -114,7 +114,7 @@ where $u$ is the sum is taken over a discrete range of $r$ between $r_{\text{min
 
 Firstly, we can test whether one cell type tends to be more localised with another cell type in one condition compared to the other. This can be done using the `spicy()` function, where we specify the `condition` parameter.
 
-In this example, we want to see whether or not neutrophils (`to`) tend to be found around CD8 T cells (`from`) in compartmentalised tumours compared to cold tumours. Given that there are 3 conditions, we can specify the desired conditions by setting the order of our `condition` factor. `spicy` will choose the first level of the factor as the base condition and the second level as the comparison condition. `spicy` will also naturally coerce the `condition` column into a factor if it is not already a factor. The column containing cell type annotations can be specified using the `cellTypeCol` argument. By default, `spicy` uses the column named `cellType` in the `SpatialExperiment` object.
+In this example, we want to see whether or not neutrophils (`to`) tend to be found around CD8 T cells (`from`) in compartmentalised tumours compared to cold tumours. Given that there are 3 conditions, we can specify the desired conditions by setting the order of our `condition` factor. `spicy` will choose the first level of the factor as the base condition and the second level as the comparison condition. `spicy` will also naturally coerce the `condition` column into a factor if it is not already a factor. The column containing cell type annotations can be specified using the `cellType` argument. By default, `spicy` uses the column named `cellType` in the `SpatialExperiment` object.
 
 ```{r}
 spicyTestPair <- spicy(