diff --git a/vignettes/seurat_sfe_coerce.Rmd b/vignettes/seurat_sfe_coerce.Rmd index bbe8f90..5e64de4 100644 --- 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],