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('viridis', 'inferno', 'plasma', 'magma', 'Blues', 'BuGn', 'BuPu', 'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd', 'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'cool', 'copper', 'gist_heat', 'gray', 'hot', 'pink', 'spring', 'summer', 'winter', 'BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral', 'seismic', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'gist_earth', 'terrain', 'ocean', 'gist_stern', 'brg', 'CMRmap', 'cubehelix', 'gnuplot', 'gnuplot2', 'gist_ncar', 'nipy_spectral', 'jet', 'rainbow', 'gist_rainbow', 'hsv', 'flag', 'prism'), optional
- Specifies the color map for plotting the heatmap. See
https://matplotlib.org/examples/color/colormaps_reference.html for more
details.
Returns
visualization : Visualization