diff --git a/README.md b/README.md index 7b50691..d19ff50 100644 --- a/README.md +++ b/README.md @@ -47,9 +47,9 @@ The Jellyfish algorithm optimizes the readability of the visualization by pushing the emerging subclones towards the leaves of the sample tree. In practice, Jellyfish finds the [Lowest Common Ancestor](https://en.wikipedia.org/wiki/Lowest_common_ancestor) (LCA) of each -cluster (a subclone and all its descendants) in the sample tree. The LCA is -visualized as an emerging bell, indicating where the subclone first appears in -the sample tree. +clade (a subclone and all its descendants) in the sample tree. The LCA subclone +is visualized as an emerging bell, indicating where the subclone first appears +in the sample tree. Each sample without an explicit parent is considered a child of the _inferred root_ sample. It is a virtual or hypothetical sample that is used to anchor the @@ -61,7 +61,7 @@ subclones that have been observed in multiple real samples. - Visualizes tumor phylogeny and subclonal compositions as a Jellyfish plot. - Allows visualizing both temporal and spatial relationships between samples. - Sorts samples based on the subclonal composition and divergence, effectively grouping similar samples together. -- Provides basic interactivity for exploring the plot, such as highlighting subclones and clusters upon hover or click, and displaying details in tooltips. +- Provides basic interactivity for exploring the plot, such as highlighting subclones and clades upon hover or click, and displaying details in tooltips. - Generates phylogeny-aware color schemes for subclones, inspired by [Visualizing Clonal Evolution in Cancer](http://dx.doi.org/10.1016/j.molcel.2016.05.025) by Krzywinski. - Exports the plot as publication-ready SVG or PNG files. - Adjustable layout parameters for fine-tuning the plot appearance.