Calling .index in function embedDistanceMatrix requires input to be a DataFrame.

[kmayerb]

utils/embedding.py

Lines 63 to 69 in b61935a

	def embedDistanceMatrix(dmatDf, method='kpca', n_components=2, **kwargs):
	"""Two-dimensional embedding of sequence distances in dmatDf,
	returning Nx2 x,y-coords: tsne, isomap, pca, mds, kpca, sklearn-tsne"""
	if isinstance(dmatDf, pd.DataFrame):
	dmat = dmatDf.values
	else:
	dmat = dmatDf

Note that the upper portion of the function is meant to accomodate either numpy.array or pd.DataFrame passed to dmatDf, but if numpy array is supplied then L111 will raise an error:

utils/embedding.py

Line 111 in b61935a

xyDf = pd.DataFrame(xy[:, :n_components], index=dmatDf.index, columns=np.arange(n_components))

Example

embedDistanceMatrix(dmatDf = pd.DataFrame(tr.pw_beta[0:10,:][:,0:10]), method = "mds")

👍

embedDistanceMatrix(dmatDf = tr.pw_beta[0:10,:][:,0:10], method = "mds")

👎

AttributeError: 'numpy.ndarray' object has no attribute 'index'

[kmayerb]

Possible Solution:

if isinstance(dmatDf, pd.DataFrame):
  xyDf = pd.DataFrame(xy[:, :n_components], index=dmatDf.index, columns=np.arange(n_components))
else:
  xyDf = pd.DataFrame(xy[:, :n_components], columns=np.arange(n_components))