From 0eb712099ffa3d252d827530e660ef26634dc601 Mon Sep 17 00:00:00 2001 From: Shreya Rao Date: Thu, 14 Nov 2024 10:54:29 +1100 Subject: [PATCH] update vignette to new args --- vignettes/spicyR.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/spicyR.Rmd b/vignettes/spicyR.Rmd index 7ef4979..8d9e393 100644 --- a/vignettes/spicyR.Rmd +++ b/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(