Remove ggspavis usage

prabhakarlab · Apr 9, 2024 · 0789bde · 0789bde
1 parent 16f7ea2
commit 0789bde
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Showing 15 changed files with 111 additions and 33 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Banksy
 Title: Spatial transcriptomic clustering
-Version: 0.99.9
+Version: 0.99.10
 Authors@R: c(
     person(given = "Vipul",
            family = "Singhal",
@@ -51,7 +51,6 @@ Suggests:
     scran,
     cowplot,
     ggplot2,
-    ggspavis,
     testthat (>= 3.0.0),
     harmony,
     Seurat,

diff --git a/R/misc.R b/R/misc.R
@@ -27,7 +27,11 @@
 #' rings <- simulateDataset(n_cells = 5e3, n_genes = 50, n_rings = 8)
 #' rings
 #' table(rings$cluster)
-#' ggspavis::plotSpots(rings, annotate = "cluster", size = 2)
+#' df <- cbind.data.frame(
+#'     SummarizedExperiment::colData(rings), 
+#'     SpatialExperiment::spatialCoords(rings))
+#' library(ggplot2)
+#' ggplot(df, aes(x=x, y=y, col=cluster)) + geom_point() + theme_classic()
 #'
 simulateDataset <- function(n_cells = 300,
                             n_genes = 30,

diff --git a/docs/articles/batch-correction.html b/docs/articles/batch-correction.html
diff --git a/docs/articles/figures/batch-correction-spatial-1.png b/docs/articles/figures/batch-correction-spatial-1.png
diff --git a/docs/articles/figures/multi-sample-spatial-1.png b/docs/articles/figures/multi-sample-spatial-1.png