Subcommand: heat tree

Make a tree with edges colored according to the placement mass of the samples.

Usage: gappa examine heat-tree [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
--mass-norm	TEXT:{absolute,relative}=absolute Set the per-sample normalization method. 'absolute' does not change the masses, while 'relative' normalizes them to a total mass of 1 per input jplace sample.
--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.
--max-value	FLOAT=1 Maximum value that is represented by the color scale. If not set, the maximum value in the data is used.
--clip-over	Clip (clamp) values greater than max to be inside [ min, max ]. If set, --over-color is not used to indicate values out of range.
--over-color	TEXT=#00ffff Color used to indicate values above max.
--min-value	FLOAT=0 Minimum value that is represented by the color scale. If not set, the minimum value in the data is used.
--clip-under	Clip (clamp) values less than min to be inside [ min, max ]. If set, --under-color is not used to indicate values out of range.
--under-color	TEXT=#ff00ff Color used to indicate values below min.
--clip	Clip (clamp) values to be inside [ min, max ]. This option is a shortcut to set --clip-under and --clip-over at once.
--mask-value	FLOAT=nan Mask value that identifies invalid values. Value in the data that compare equal to the mask value are colored using --mask-color. This is meant as a simple means of filtering and visualizing invalid values. If not set, no masking value is applied.
--mask-color	TEXT=#ffff00 Color used to indicate masked values.
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.
Output
--out-dir	TEXT=. Directory to write files to
--tree-file-prefix	TEXT=tree File prefix for tree files
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

The command takes one or more jplace files as input and visualizes the distribution of placements on the branches of the tree. It uses color coding to show how much placement mass there is per branch.

Important remark: If multiple jplace files are provided as input, their combined placements are visualized. It is then critical to correctly set the --mass-norm option. If set to absolute, no normalization is performed per jplace file - thus, absolute abundances are shown. However, if set to relative, the placement mass in each input file is normalized to unit mass 1.0 first, thus showing relative abundances.

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