GOPCASignatureMatrix
class¶gopca.
GOPCASignatureMatrix
(*args, **kwargs)¶A GO-PCA signature matrix (the result of a GO-PCA run).
filter_collection_signatures
(corr_thresh=0.9, source=None)¶Filter signatures by collection.
filter_signatures
(corr_thresh, inplace=False)¶Remove “redundant” signatures.
from_signatures
(signatures, standardize=False, center=True, use_median=True, cluster_signatures=True, signature_cluster_metric=u'correlation', cluster_samples=True, sample_cluster_metric=u'euclidean', cluster_method=u'average')¶Generate a GO-PCA signature matrix from individual signatures.
The GO-PCA signature matrix contains the expression levels of all
signatures (rows) generated, across all samples (columns) in the
analysis. See the documentation of the GOPCASignature
class for
details on how signature expression levels are calculated.
Parameters: |
|
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get_figure
(heatmap_kw=None, **kwargs)¶Generate a plotly figure showing the signature matrix as a heatmap.
This is a shortcut for
SignatureMatrix.get_heatmap(...).get_figure(...)
.
See ExpHeatmap.get_figure()
for keyword arguments.
Parameters: | heatmap_kw (dict or None) – If not None, dictionary containing keyword arguments to be passed
to the ExpHeatmap constructor. |
---|---|
Returns: | The plotly figure. |
Return type: | plotly.graph_objs.Figure |
get_heatmap
(max_name_length=40, include_id=False, highlight_sig=None, highlight_source=None, matrix_kw=None, colorbar_label=u'Signature expression<br>(log<sub>2</sub>-scale)', annotation_transparency=0.8)¶Generate an ExpHeatMap
instance.
get_signature
(name, pc=None, i=None)¶Look up a signature by name, PC, and index.
get_signature_labels
(**kwargs)¶Generate a list of GO-PCA signature labels (convenience function).
Returns: | List of signature labels. |
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Return type: | list of str |
hash
¶An MD5 hash string for the signature.
n
¶The number of samples in the matrix.
q
¶The number of signatures in the matrix.
signature_labels
¶The list of signature labels.
signatures
¶This returns the list of signatures (as a pandas.Index
object).