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docs: fix README
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tuner committed Jan 23, 2025
1 parent f21de38 commit 79fad1e
Showing 1 changed file with 6 additions and 5 deletions.
11 changes: 6 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
@@ -63,7 +63,7 @@ y <- infer.clonal.models(...)
y <- convert.consensus.tree.clone.to.branch(y)

# Plot the results
extract_tables_from_clonevol(y, model = 1)) |>
extract_tables_from_clonevol(y, model = 1) |>
jellyfisher()
```

@@ -73,7 +73,8 @@ By default, all samples that have no explicit parent are children of the
_inferred root_ sample. You can customize the parent-child relationships by
modifying the `parent` column in the `samples` data frame before plotting.

You can also modify the relationships using the `set_parents` function.
You can also modify the relationships with ease using the `set_parents`
function.

For example, if you have three samples, A, B, and C, they will have the
following relationships by default:
@@ -90,7 +91,7 @@ With the explicit parents, you can customize the relationships:
tables |>
set_parents(list(
# The parent of C is B
C = "B"
"C" = "B"
) |>
jellyfisher()
```
@@ -119,13 +120,13 @@ after building the Jellyfish dependency.

## About

Copyright (c) 2025 Kari Lavikka. MIT license, see [LICENSE](LICENSE) for details.
Copyright (c) 2025 Kari Lavikka. MIT license, see [LICENSE.md](LICENSE.md) for details.

Jellyfisher is developed in [The Systems Biology of Drug Resistance in
Cancer](https://www.helsinki.fi/en/researchgroups/systems-biology-of-drug-resistance-in-cancer)
group at the [University of Helsinki](https://www.helsinki.fi/en).

This project has received funding from the European Union's Horizon 2020
research and innovation programme under grant agreement No. 965193
research and innovation programme under grant agreements No. 965193
([DECIDER](https://www.deciderproject.eu/)) and No. 847912
([RESCUER](https://www.rescuer.uio.no/)).

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