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dendrogram-heatmap: Dendrogram heatmap.ΒΆ

Docstring:

Usage: qiime gneiss dendrogram-heatmap [OPTIONS]

  Visualize the feature table as a heatmap, with samples sorted along a
  specified categorical metadata column and features clustered together
  specified by the tree.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  The feature table that will be plotted as a
                                  heatmap. This table is assumed to have
                                  strictly positive values.  [required]
  --i-tree ARTIFACT PATH Hierarchy
                                  A hierarchy of feature identifiers where
                                  each tipcorresponds to the feature
                                  identifiers in the table. This tree can
                                  contain tip ids that are not present in the
                                  table, but all feature ids in the table must
                                  be present in this tree.  [required]
  --m-metadata-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata.
                                  [required]
  --m-metadata-column MetadataColumn[Categorical]
                                  Column from metadata file or artifact
                                  viewable as metadata. Categorical metadata
                                  column to group the samples.  [required]
  --p-pseudocount FLOAT           The pseudocount to add to avoid division by
                                  zero.  [default: 0.5]
  --p-ndim INTEGER                Number of dimensions to highlight.
                                  [default: 10]
  --p-method [clr|log]            Specifies how the data should be normalized
                                  for display.Options include 'log' or 'clr'
                                  (default='clr').  [default: clr]
  --p-color-map [Pastel1|ocean|PuBu|nipy_spectral|YlGn|Set1|gnuplot|RdYlBu|bone|seismic|Greens|Accent|hsv|gist_earth|coolwarm|Dark2|Set2|Purples|PuBuGn|viridis|rainbow|Pastel2|magma|PuOr|Paired|gnuplot2|RdPu|brg|Blues|YlGnBu|Greys|bwr|afmhot|RdBu|PuRd|spring|pink|Vega20|terrain|PRGn|BuGn|Oranges|winter|Set3|Vega20b|GnBu|PiYG|CMRmap|copper|flag|Reds|gist_stern|gist_rainbow|RdGy|hot|gist_ncar|YlOrBr|cool|OrRd|gray|jet|Spectral|prism|BuPu|autumn|cubehelix|RdYlGn|inferno|BrBG|YlOrRd|Vega20c|gist_heat|summer|Vega10|plasma]
                                  Specifies the color map for plotting the
                                  heatmap. See https://matplotlib.org/examples
                                  /color/colormaps_reference.html for more
                                  details.  [default: viridis]
  --o-visualization VISUALIZATION PATH
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.gneiss.visualizers import dendrogram_heatmap

Docstring:

Dendrogram heatmap.

Visualize the feature table as a heatmap, with samples sorted along a
specified categorical metadata column and features clustered together
specified by the tree.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table that will be plotted as a heatmap. This table is
    assumed to have strictly positive values.
tree : Hierarchy
    A hierarchy of feature identifiers where each tipcorresponds to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
metadata : MetadataColumn[Categorical]
    Categorical metadata column to group the samples.
pseudocount : Float, optional
    The pseudocount to add to avoid division by zero.
ndim : Int, optional
    Number of dimensions to highlight.
method : Str % Choices({'clr', 'log'}), optional
    Specifies how the data should be normalized for display.Options include
    'log' or 'clr' (default='clr').
color_map : Str % Choices({'Accent', 'Blues', 'BrBG', 'BuGn', 'BuPu', 'CMRmap', 'Dark2', 'GnBu', 'Greens', 'Greys', 'OrRd', 'Oranges', 'PRGn', 'Paired', 'Pastel1', 'Pastel2', 'PiYG', 'PuBu', 'PuBuGn', 'PuOr', 'PuRd', 'Purples', 'RdBu', 'RdGy', 'RdPu', 'RdYlBu', 'RdYlGn', 'Reds', 'Set1', 'Set2', 'Set3', 'Spectral', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'brg', 'bwr', 'cool', 'coolwarm', 'copper', 'cubehelix', 'flag', 'gist_earth', 'gist_heat', 'gist_ncar', 'gist_rainbow', 'gist_stern', 'gnuplot', 'gnuplot2', 'gray', 'hot', 'hsv', 'inferno', 'jet', 'magma', 'nipy_spectral', 'ocean', 'pink', 'plasma', 'prism', 'rainbow', 'seismic', 'spring', 'summer', 'terrain', 'viridis', 'winter'}), optional
    Specifies the color map for plotting the heatmap. See
    https://matplotlib.org/examples/color/colormaps_reference.html for more
    details.

Returns
-------
visualization : Visualization