SMI plotting function¶
This is the SMI plotting function.
-
hoggormplot.SMI_plot.
plotSMI
(smi, pc='max', significance=True, X1name='X1', X2name='X2', B=10000, fontscale=1, figsize=None)¶ Diamond plot for Similarity of matrices index (SMI)
Parameters: - smi (SMI class object) – the SMI results to visualize.
- pc (list, optional) – the number of components to display, default is ‘max’ = all components.
- significance (boolean, optional) – plotting of significance symbols, added by default.
- X1name (list, optional) – name of the first data set, default = ‘X1’.
- X2name (list, optional) – name of the second data set, default = ‘X2’.
- B (int, optional) – number of permutations to use with significance testing.
- fontscale (double, optional) – scaling parameter for significance symbols and component labels.
- figsize (tuple, optional) – Sets figure width and height in inches
Examples
>>> import numpy as np >>> import hoggorm as ho >>> import hoggormplot as hop
>>> X1 = ho.center(np.random.rand(100,300)) >>> U, s, V = np.linalg.svd(X1, 0) >>> X2 = np.dot(np.dot(np.delete(U, 2, 1), np.diag(np.delete(s, 2))), np.delete(V, 2, 0))
>>> smiOP = ho.SMI(X1, X2, ncomp1=10, ncomp2=10) >>> print(smiOP.smi[:4,:4])
>>> hop.plotSMI(smiOP)