Use <- instead of = for consistency

Author: mblue9

vignettes/tidytranscriptomics_case_study.Rmd

@@ -387,22 +387,22 @@ For comparison, we show the alternative using base R and Seurat
 
 ```{r eval = FALSE}
 
-counts_positive = 
+counts_positive <- 
   GetAssayData(seurat_obj, assay="SCT")[c("CD3D", "TRDC", "TRGC1", "TRGC2"),] |> 
   colSums() |> 
   scales::rescale(to=c(0,1)) 
 
-counts_negative = 
+counts_negative <- 
   GetAssayData(seurat_obj, assay="SCT")[c("CD8A", "CD8B"),] |> 
   colSums()  |> 
   scales::rescale(to=c(0,1)) 
 
-seurat_obj$signature_score = counts_positive - counts_negative
+seurat_obj$signature_score <- counts_positive - counts_negative
 
-p = FeaturePlot(seurat_obj, features = "signature_score")
+p <- FeaturePlot(seurat_obj, features = "signature_score")
 
 # This is not reproducible (in contrast to tidygate)
-seurat_obj$within_gate = colnames(seurat_obj) %in% CellSelector(plot = p)
+seurat_obj$within_gate <- colnames(seurat_obj) %in% CellSelector(plot = p)
 
 seurat_obj |> 
   subset(within_gate == TRUE) |>
@@ -429,7 +429,7 @@ single_cell_object |>
 We'll demonstrate creating a 3D plot using some data that has 3 UMAP dimensions.
 
 ```{r umap plot 2, message = FALSE, warning = FALSE}
-pbmc = iscb2022tidytranscriptomics::seurat_obj_UMAP3
+pbmc <- iscb2022tidytranscriptomics::seurat_obj_UMAP3
 
 pbmc |>