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Subcommand: heat tree
Make a tree with edges colored according to the placement mass of the samples.
Usage: gappa examine heat-tree [options]
Input | |
---|---|
--jplace-path |
Required. TEXT:PATH(existing) ... List of jplace files or directories to process. For directories, only files with the extension .jplace 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 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 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 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 |
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.
Module analyze
- correlation
- dispersion
- edgepca
- imbalance-kmeans
- krd
- phylogenetic-kmeans
- placement-factorization
- squash
Module edit
Module examine
Module prepare
Module simulate
Module tools