update xenium pre-release tutorial

drieslab · Nov 18, 2024 · c58374b · c58374b
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diff --git a/vignettes/images/xenium_breast_cancer/1_spatplot.png b/vignettes/images/xenium_breast_cancer/1_spatplot.png
diff --git a/vignettes/images/xenium_breast_cancer/2_HVF.png b/vignettes/images/xenium_breast_cancer/2_HVF.png
diff --git a/vignettes/images/xenium_breast_cancer/3a_screePlot.png b/vignettes/images/xenium_breast_cancer/3a_screePlot.png
diff --git a/vignettes/images/xenium_breast_cancer/3b_PCA.png b/vignettes/images/xenium_breast_cancer/3b_PCA.png
diff --git a/vignettes/images/xenium_breast_cancer/4a_tSNE.png b/vignettes/images/xenium_breast_cancer/4a_tSNE.png
diff --git a/vignettes/images/xenium_breast_cancer/4b_UMAP.png b/vignettes/images/xenium_breast_cancer/4b_UMAP.png
diff --git a/vignettes/images/xenium_breast_cancer/5_umap_leiden.png b/vignettes/images/xenium_breast_cancer/5_umap_leiden.png
diff --git a/vignettes/images/xenium_breast_cancer/6_spat_leiden.png b/vignettes/images/xenium_breast_cancer/6_spat_leiden.png
diff --git a/vignettes/images/xenium_breast_cancer/7_polys.png b/vignettes/images/xenium_breast_cancer/7_polys.png
diff --git a/vignettes/images/xenium_breast_cancer/8_subset_in_situ.png b/vignettes/images/xenium_breast_cancer/8_subset_in_situ.png
diff --git a/vignettes/images/xenium_breast_cancer/gpoints.png b/vignettes/images/xenium_breast_cancer/gpoints.png
diff --git a/vignettes/images/xenium_breast_cancer/gpoints_blnk.png b/vignettes/images/xenium_breast_cancer/gpoints_blnk.png
diff --git a/vignettes/images/xenium_breast_cancer/gpoints_expr.png b/vignettes/images/xenium_breast_cancer/gpoints_expr.png
diff --git a/vignettes/images/xenium_breast_cancer/gpoints_ngcode.png b/vignettes/images/xenium_breast_cancer/gpoints_ngcode.png
diff --git a/vignettes/images/xenium_breast_cancer/gpoints_ngprbe.png b/vignettes/images/xenium_breast_cancer/gpoints_ngprbe.png
diff --git a/vignettes/images/xenium_breast_cancer/gpolys.png b/vignettes/images/xenium_breast_cancer/gpolys.png
diff --git a/vignettes/images/xenium_breast_cancer/gpolys_centroids.png b/vignettes/images/xenium_breast_cancer/gpolys_centroids.png
diff --git a/vignettes/images/xenium_breast_cancer/he_prev.png b/vignettes/images/xenium_breast_cancer/he_prev.png
diff --git a/vignettes/images/xenium_breast_cancer/her2_example.png b/vignettes/images/xenium_breast_cancer/her2_example.png
diff --git a/vignettes/images/xenium_breast_cancer/her2_prev.png b/vignettes/images/xenium_breast_cancer/her2_prev.png
diff --git a/vignettes/images/xenium_breast_cancer/if_prev.png b/vignettes/images/xenium_breast_cancer/if_prev.png
diff --git a/vignettes/images/xenium_breast_cancer/large_preview.png b/vignettes/images/xenium_breast_cancer/large_preview.png
diff --git a/vignettes/images/xenium_breast_cancer/leiden_tsne.png b/vignettes/images/xenium_breast_cancer/leiden_tsne.png
diff --git a/vignettes/images/xenium_breast_cancer/leiden_umap.png b/vignettes/images/xenium_breast_cancer/leiden_umap.png
diff --git a/vignettes/images/xenium_breast_cancer/pca.png b/vignettes/images/xenium_breast_cancer/pca.png
diff --git a/vignettes/images/xenium_breast_cancer/poly_example.png b/vignettes/images/xenium_breast_cancer/poly_example.png
diff --git a/vignettes/images/xenium_breast_cancer/poly_leiden.png b/vignettes/images/xenium_breast_cancer/poly_leiden.png
diff --git a/vignettes/images/xenium_breast_cancer/scatter_example.png b/vignettes/images/xenium_breast_cancer/scatter_example.png
diff --git a/vignettes/images/xenium_breast_cancer/scree.png b/vignettes/images/xenium_breast_cancer/scree.png
diff --git a/vignettes/images/xenium_breast_cancer/spat_leiden.png b/vignettes/images/xenium_breast_cancer/spat_leiden.png
diff --git a/vignettes/images/xenium_breast_cancer/tsne.png b/vignettes/images/xenium_breast_cancer/tsne.png
diff --git a/vignettes/images/xenium_breast_cancer/umap.png b/vignettes/images/xenium_breast_cancer/umap.png
diff --git a/vignettes/images/xenium_breast_cancer/zoomin.png b/vignettes/images/xenium_breast_cancer/zoomin.png
diff --git a/vignettes/visualizations.Rmd b/vignettes/visualizations.Rmd
@@ -12,6 +12,12 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+relevant options
+```
+giotto.plot_img_max_sample)
+giotto.plot_point_raster
+```
+
 
 # Dataset explanation