update seurat_sfe_coerce.Rmd

pachterlab · May 30, 2024 · 0066e7c · 0066e7c
1 parent 495b15e
commit 0066e7c
Showing 1 changed file with 4 additions and 20 deletions.
diff --git a/vignettes/seurat_sfe_coerce.Rmd b/vignettes/seurat_sfe_coerce.Rmd
@@ -144,7 +144,7 @@ plotSpatialFeature(sfe_conv_vis2, exprs_values = "counts",
 sfe_vishd <-
   toSpatialFeatureExperiment(x = obj_vishd, 
                              image_scalefactors = "lowres",
-                             unit = "micron",
+                             unit = "micron", #"full_res_image_pixel",
                              BPPARAM = BPPARAM)
 sfe_vishd
 getMeta(sfe_vishd) %>% str
@@ -357,23 +357,6 @@ plotSpatialFeature(sfe_vis_multi, exprs_values = "counts",
                    scattermore = FALSE
                   )
 ```
-## TODO: Convert multiple samples/FOVs - Visium HD (only "counts" present in both samples)
-```{r}
-# slim down Visium HD to keep only "counts" for all FOVs/samples
-if (!exists("obj_vishd_multi_slim"))
-  obj_vishd_multi_slim <- 
-    DietSeurat(obj_vishd_multi, layers = "counts", assays = Assays(obj_vishd_multi)) %>% 
-    UpdateSeuratObject()
-sfe_vishd_multi <-
-  toSpatialFeatureExperiment(x = obj_vishd_multi_slim, 
-                             image_scalefactors = "lowres",
-                             unit = "micron",
-                             BPPARAM = BPPARAM)
-sfe_vishd_multi
-getMeta(sfe_vishd_multi) %>% str
-```
-
-
 
 ## TODO: Convert multiple samples/FOVs - Visium HD
 ```{r}
@@ -394,11 +377,12 @@ plotSpatialFeature(sfe_vishd_multi, exprs_values = "counts",
                    dark = TRUE,
                    show_axes = TRUE,
                    sample_id = sampleIDs(sfe_vishd_multi)[1],
-                   scattermore = FALSE
+                   scattermore = TRUE
                   )
+# 16 microns better plotted using polygons
 plotSpatialFeature(sfe_vishd_multi, exprs_values = "counts",
                    features = rownames(sfe_vishd_multi)[1], 
-                   #size = 1, colGeometryName = "spotPoly",
+                   size = 0, colGeometryName = "spotPoly",
                    dark = TRUE,
                    show_axes = TRUE,
                    sample_id = sampleIDs(sfe_vishd_multi)[2],