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. With absolute, the total mass is not changed, so that input jplace samples with more pqueries have a higher influence on the result. With relative, the total mass of each sample is normalized to 1.0, so that each sample has the same influence on the result.
--point-mass	FLAG Treat every pquery as a point mass concentrated on the highest-weight placement. In other words, ignore all but the most likely placement location (the one with the highest LWR), and set its LWR to 1.0.
--ignore-multiplicities	FLAG Set the multiplicity of each pquery to 1.0. The multiplicity is the equvalent of abundances for placements.
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 comma-separated list of colors. Colors can be specified in the format #rrggbb using hex values, or by web color names.
--reverse-color-list	FLAG If set, the order of colors of the --color-list is reversed.
--under-color	TEXT=#ff00ff Color used to indicate values below the min value. Color can be specified in the format #rrggbb using hex values, or by web color names.
--clip-under	FLAG Clip (i.e., clamp) values less than min to be inside [ min, max ], by setting values that are too low to the specified min value. If set, --under-color is not used to indicate values out of range.
--over-color	TEXT=#00ffff Color used to indicate values above the max value. Color can be specified in the format #rrggbb using hex values, or by web color names.
--clip-over	FLAG Clip (i.e., clamp) values greater than max to be inside [ min, max ], by setting values that are too high to the specified max value. If set, --over-color is not used to indicate values out of range.
--clip	FLAG Clip (i.e., clamp) values to be inside [ min, max ], by setting values outside of that interval to the nearest boundary of it. This option is a shortcut to set --clip-under and --clip-over at once.
--mask-color	TEXT=#ffff00 Color used to indicate masked or invalid values, such as infinities or NaNs. Color can be specified in the format #rrggbb using hex values, or by web color names.
--log-scaling	FLAG If set, the sequential color list is logarithmically scaled instead of linearily.
--min-value	FLOAT=0 Minimum value that is represented by the color scale. If not set, the minimum value of the data is used.
--max-value	FLOAT=1 Maximum value that is represented by the color scale. If not set, the maximum value of the data is used.
--mask-value	FLOAT=nan Mask value that identifies invalid values (in addition to infinities and NaN values, which are always considered invalid, and hence always masked). Value of 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.
Output
--out-dir	TEXT=. Directory to write files to
--file-prefix	TEXT File prefix for output files
--file-suffix	TEXT File suffix for output files
Tree Output
--write-newick-tree	FLAG If set, the tree is written to a Newick file.
--write-nexus-tree	FLAG If set, the tree is written to a Nexus file.
--write-phyloxml-tree	FLAG If set, the tree is written to a Phyloxml file.
--write-svg-tree	FLAG 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	FLAG If set, the tree is ladderized.
Global Options
--allow-file-overwriting	FLAG Allow to overwrite existing output files instead of aborting the command.
--verbose	FLAG 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