making reproducible vignette

rpolicastro · May 13, 2020 · f124570 · f124570
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diff --git a/README.md b/README.md
@@ -20,22 +20,25 @@ This library pulls the meta-data from a seurat object for its analysis.
 This means that you must first process your data in seurat.
 Seurat has various [vignettes](https://satijalab.org/seurat/vignettes.html) to get you started.
 
-Once you have a seurat object, you are ready to get started. This first step is to create the
-analysis object.
+Once you have a seurat object, you are ready to get started.
+We'll first load some example data for the vignette, adn create the analysis object.
 
 ```
 library("scProportionTest")
 
-prop_test <- sc_utils(seurat_object)
+seurat_data <- system.file("extdata", "example_data.RDS", package = "scProportionTest")
+seurat_data <- readRDS(seurat_data)
+
+prop_test <- sc_utils(seurat_data)
 ```
 
 Once the object is created, the permutation testing and bootstrapping can be run.
 
 ```
 prop_test <- permutation_test(
-	prop_test, cluster_identity = "final_clusters",
-	sample_1 = "EV", sample_2 = "KD",
-	sample_identity = "orig.ident",
+	prop_test, cluster_identity = "custom_clusters",
+	sample_1 = "HT29_EV", sample_2 = "HT29_LSD1_KD",
+	sample_identity = "orig.ident"
 )
 ```
 
@@ -44,3 +47,5 @@ A point-range plot of the results can then be created.
 ```
 permutation_plot(prop_test)
 ```
+
+![example_plot](inst/images/example_plot.png)
diff --git a/inst/extdata/example_data.RDS b/inst/extdata/example_data.RDS
diff --git a/inst/images/example_plot.png b/inst/images/example_plot.png