diff --git a/vignettes/a02_sampling_simulation.Rmd b/vignettes/a02_sampling_simulation.Rmd index 9f325263..49db3ad6 100644 --- a/vignettes/a02_sampling_simulation.Rmd +++ b/vignettes/a02_sampling_simulation.Rmd @@ -332,11 +332,11 @@ Sample again and plot the tissue ```{r, fig.height=4, fig.width=3} -sim$sample_cells("A2", bottom_left = c(480, 480), - top_right = c(480 + bbox_width, 480 + bbox_width)) +sim$sample_cells("A2", bottom_left = c(250, 500), + top_right = c(250 + bbox_width, 500 + bbox_width)) -sim$sample_cells("B2", bottom_left = c(500, 500), - top_right = c(500 + bbox_width, 500 + bbox_width)) +sim$sample_cells("B2", bottom_left = c(500, 165), + top_right = c(500 + bbox_width, 165 + bbox_width)) plot_tissue(sim, num_of_bins = 500) plot_muller(sim) @@ -346,12 +346,15 @@ Now we show the cell division tree, which starts being rather complicated ```{r, fig.height=12, fig.width=17} -plot_forest(sim$get_samples_forest()) +forest <- sim$get_samples_forest() + +plot_forest(forest) %>% + annotate_forest(forest) ``` ## More complex example -Some functionalities allow for a smarter sampling and more advanced +Some features allow for a smarter sampling and more advanced visualisation. We build a tumour with three populations, branching.