pyani.pyani_graphics.mpl package

Module contents

Code to implement MatPLotLib graphics output for ANI analyses.

pyani.pyani_graphics.mpl.add_colorbar(dfr, fig, dend, params, orientation='row')

Add class colorbars to Matplotlib heatmap.

Parameters:

• dfr –
• fig –
• dent –
• params –
• orientation –

pyani.pyani_graphics.mpl.add_colorscale(fig, heatmap_gs, ax_map, params, title=None)

Add colour scale to heatmap.

Parameters:

• fig –
• heatmap_gs –
• ax_map –
• params –
• title –

pyani.pyani_graphics.mpl.add_dendrogram(dfr, fig, params, heatmap_gs, orientation='col')

Return a dendrogram and corresponding gridspec, attached to the fig.

Parameters:

• dfr – Pandas DataFrame describing input data
• fig – matplotlib Fig that holds graphical output
• params – pyani_graphics.Params object
• heatmap_gs – matplotlib GridSpec for this dendrogram
• orientation – str, “row” or “col”

Modifies the fig in-place. Orientation is either ‘row’ or ‘col’ and determines location and orientation of the rendered dendrogram.

We expect that the row/column index values should be ordered identically. If they are not, the dendrogram will not match labels

pyani.pyani_graphics.mpl.add_labels(heatmap_axes, rowlabels, collabels, params)

Add labels to Matplotlib heatmap axes, in-place.

Parameters:

• heatmap_axes –
• rowlabels –
• collabels –
• params –

pyani.pyani_graphics.mpl.clean_axis(axis)

Remove ticks, tick labels, and frame from axis.

Parameters:axis –

pyani.pyani_graphics.mpl.distribution(dfr, outfilename, matname, title=None)

Return matplotlib distribution plot for matrix.

Parameters:

• dfr – DataFrame with results matrix
• outfilename – Path to output file for writing
• matname – str, type of matrix being plotted
• title – str, optional title

pyani.pyani_graphics.mpl.get_heatmap_axes(dfr, fig, heatmap_gs)

Return axis for Matplotlib heatmap.

Parameters:

• dfr –
• fig –
• heatmap_gs –

pyani.pyani_graphics.mpl.heatmap(dfr, outfilename=None, title=None, params=None)

Return matplotlib heatmap with cluster dendrograms.

Parameters:

• dfr – pandas DataFrame with relevant data
• outfilename – path to output file (indicates output format)
• params – a list of parameters for plotting: [colormap, vmin, vmax]
• labels – dictionary of alternative labels, keyed by default sequence labels
• classes – dictionary of sequence classes, keyed by default sequence labels

pyani.pyani_graphics.mpl.scatter(dfr1, dfr2, outfilename=None, matname1='identity', matname2='coverage', title=None, params=None)

Return matplotlib scatterplot.

Parameters:

• dfr1 – pandas DataFrame with x-axis data
• dfr2 – pandas DataFrame with y-axis data
• outfilename – path to output file (indicates output format)
• matname1 – name of x-axis data
• matname2 – name of y-axis data
• title – title for the plot
• params – a list of parameters for plotting: [colormap, vmin, vmax]