diff --git a/vignettes/visiumStitched.Rmd b/vignettes/visiumStitched.Rmd index a293555..9109aec 100644 --- a/vignettes/visiumStitched.Rmd +++ b/vignettes/visiumStitched.Rmd @@ -314,7 +314,10 @@ the overlap among capture areas: ```{r "array_plot_orig"} ## Plot positions of default array coordinates, before overwriting with more -## meaningful values +## meaningful values. Use custom colors for each capture area +ca_colors = c("#A33B20", "#e7bb41", "#3d3b8e") +names(ca_colors) = c("V13B23-283_C1", "V13B23-283_D1", "V13B23-283_A1") + colData(spe) |> as_tibble() |> filter(in_tissue) |> @@ -324,7 +327,7 @@ colData(spe) |> ) ) + geom_point(alpha = 0.3) + - coord_fixed() + scale_color_manual(values = ca_colors) ``` Let's contrast this with the array coordinates recomputed by `visiumStitched`. @@ -345,7 +348,7 @@ colData(spe) |> ) ) + geom_point(alpha = 0.3) + - coord_fixed() + scale_color_manual(values = ca_colors) ``` An important downstream application of these array coordinates, is that it enables