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Updated "Tissue sampling" article
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- updated two sample positions
- added annotation to a forest plot
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albertocasagrande committed Nov 25, 2023
1 parent 086e0e5 commit 992c145
Showing 1 changed file with 9 additions and 6 deletions.
15 changes: 9 additions & 6 deletions vignettes/a02_sampling_simulation.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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.
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