Example data based on the following publication: Lahtinen A, Lavikka K, Virtanen A, et al. Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma. Cancer Cell. 2023;41(6):1103-1117.e12. doi:10.1016/j.ccell.2023.04.017
Format
jellyfisher_example_tables
A named list of data frames containing the following tables:
samplesA data frame with sample data. Columns are:
- sample
specifies the unique identifier for each sample. (string)
- displayName
allows for specifying a custom name for each sample. If the column is omitted, the
samplecolumn is used as the display name. (string, optional)- rank
specifies the position of each sample in the Jellyfish plot. For example, different stages of a disease can be ranked in chronological order: diagnosis (1), interval (2), and relapse (3). The zeroth rank is reserved for the root of the sample tree. Ranks can be any integer, and unused ranks are automatically excluded from the plot. If the
rankcolumn is (integer)- parent
identifies the parent sample for each entry. Samples without a specified parent are treated as children of an imaginary root sample. (string)
phylogenyA data frame with phylogeny data. Columns are:
- subclone
specifies subclone IDs, which can be any string. (string)
- parent
designates the parent subclone. The subclone without a parent is considered the root of the phylogeny. (string)
- color
specifies the color for the subclone. If the column is omitted, colors will be generated automatically. (string, optional)
- branchLength
specifies the length of the branch leading to the subclone. The length may be based on, for example, the number of unique mutations in the subclone. The branch length is shown in the Jellyfish plot's legend as a bar chart. It is also used when generating a phylogeny-aware color scheme. (number)
compositionsA data frame with subclonal compositions. Columns are:
- sample
specifies the sample ID. (string)
- subclone
specifies the subclone ID. (string)
- clonalPrevalence
specifies the clonal prevalence of the subclone in the sample. The clonal prevalence is the proportion of the subclone in the sample. The clonal prevalences in a sample must sum to 1. (number)