Subcommand: imbalance kmeans

Run Imbalance k-means clustering on a set of samples.

Usage: gappa analyze imbalance-kmeans [options]

Options

Input
--jplace-path	Required. TEXT:PATH(existing)=[] ... List of jplace files or directories to process. For directories, only files with the extension `.jplace[.gz]` are processed.
Settings
--k	Required. TEXT Number of clusters to find. Can be a comma-separated list of multiple values or ranges for k, such as `"1-5,8,10,12"`
--write-overview-file	If provided, a table file is written that summarizes the average distance and variance of the clusters for each k. Useful for elbow plots.
--point-mass	Treat every pquery as a point mass concentrated on the highest-weight placement.
--ignore-multiplicities	Set the multiplicity of each pquery to 1.
Color
--color-list	TEXT=BuPuBk List of colors to use for the palette. Can either be the name of a color list, a file containing one color per line, or an actual list of colors.
--reverse-color-list	If set, the `--color-list` is reversed.
--log-scaling	If set, the sequential color list is logarithmically scaled instead of linearily.
Output
--out-dir	TEXT=. Directory to write files to
--file-prefix	TEXT=ikmeans_ File prefix for output files
--file-suffix	TEXT File suffix for output files
Tree Output
--write-newick-tree	If set, the tree is written to a Newick file.
--write-nexus-tree	If set, the tree is written to a Nexus file.
--write-phyloxml-tree	If set, the tree is written to a Phyloxml file.
--write-svg-tree	If set, the tree is written to a Svg file.
Svg Tree Output
--svg-tree-shape	TEXT:{circular,rectangular}=circular Shape of the tree.
--svg-tree-type	TEXT:{cladogram,phylogram}=cladogram Type of the tree.
--svg-tree-stroke-width	FLOAT=5 Svg stroke width for the branches of the tree.
--svg-tree-ladderize	If set, the tree is ladderized.
Global Options
--allow-file-overwriting	Allow to overwrite existing output files instead of aborting the command.
--verbose	Produce more verbose output.
--threads	UINT Number of threads to use for calculations.
--log-file	TEXT Write all output to a log file, in addition to standard output to the terminal.

Description

Imbalance k-means has almost the same usage as Phylogenetic k-means. See there for details. The difference is in the distance measure being used, which is a simple Euclidean distance of the edge imbalances of the samples, instead of using the more involved Phylogenetic KR distance between samples.

Citation

When using this method, please do not forget to cite

Lucas Czech, Pierre Barbera, Alexandros Stamatakis. Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data. Bioinformatics, 2020. doi:10.1093/bioinformatics/btaa070

Lucas Czech, Alexandros Stamatakis. Scalable Methods for Analyzing and Visualizing Phylogenetic Placement of Metagenomic Samples. PLOS ONE, 2019. doi:10.1371/journal.pone.0217050