vignettes/subset_giotto.Rmd
subset_giotto.Rmd
There are several ways to subset a Giotto object or visualize a subset of the data. Here we will use the already analyzed Visium 10X brain dataset object to:
Figures may not be identical, because examples might have been updated, but the subsetting principles remain the same.
spatDimPlot(visium_brain, cell_color = 'leiden_clus',
plot_alignment = 'horizontal', spat_point_size = 2)
spatDimPlot(visium_brain,
cell_color = 'leiden_clus', select_cell_groups = '4',
plot_alignment = 'horizontal', spat_point_size = 2)
spatDimPlot(visium_brain,
cell_color = 'leiden_clus', select_cell_groups = '4', show_other_cells = F,
plot_alignment = 'horizontal', spat_point_size = 2)
spatDimPlot(visium_brain, cell_color = 'HMRF_k12_b.1',
plot_alignment = 'horizontal', spat_point_size = 2)
metadata = pDataDT(visium_brain)
subset_cell_IDs = metadata[leiden_clus %in% c(4, 5, 8, 13)]$cell_ID
visium_brain_small = subsetGiotto(visium_brain, cell_ids = subset_cell_IDs)
spatDimPlot(visium_brain_small,
cell_color = 'leiden_clus',
plot_alignment = 'horizontal', spat_point_size = 2.5)
spatDimPlot(visium_brain_small,
cell_color = 'nr_genes', color_as_factor = F,
plot_alignment = 'horizontal', spat_point_size = 2.5)
DG_subset = subsetGiottoLocs(visium_brain,
x_max = 6500, x_min = 3000,
y_max = -2500, y_min = -5500)
spatDimPlot(DG_subset,
cell_color = 'leiden_clus',
plot_alignment = 'horizontal', spat_point_size = 4,
save_param = list(save_name = '6_DG_loc_subset', base_height = 4))