# mgkit.plots.abund module¶

New in version 0.1.15.

Module to plot relative abundances in a 1D or 3D projection

mgkit.plots.abund.col_func_firstel(key, colors=None)
mgkit.plots.abund.col_func_name(key, func=None, colors=None)
mgkit.plots.abund.col_func_taxon(taxon_id, taxonomy, anc_ids, colpal)
mgkit.plots.abund.draw_1d_grid(ax, labels=['LAM', 'SAM'], fontsize=22)

Changed in version 0.2.0: reworked internals and changed defaults

Draws a 1D axis, to display propotions.

Parameters: ax – an axis instance labels (iterable) – list of string to be put for the axes fontsize (float) – font size for the labels, the tick font size is equal to 0.75 * fontsize
mgkit.plots.abund.draw_axis_internal_triangle(ax, color='r', linewidth=2.0)

New in version 0.2.5.

Draws a triangle that indicates the 50% limit for all 3 samples

Parameters: ax – axis to use color (str, float, tuple) – color used to draw the triangle linewidth (float) – line width
mgkit.plots.abund.draw_circles(ax, data, col_func=<function col_func_name>, csize=200, alpha=0.5, sizescale=None, order=None, linewidths=0.0, edgecolor='none')

Changed in version 0.2.0: changed internals and added return value

Draws a scatter plot over either a planar-simplex projection, if the number of coordinates is 3, or in a 1D axis.

If the number of coordinates is 3, project_point() is used to project the point in 2 coordinates. The coordinates are converted in proportions internally.

Parameters: ax – axis to plot on data (pandas.DataFrame) – a DataFrame with 2 for a 1D plot or 3 columns for a planar-simplex col_func (func) – a function that accept a parameter, an element of the DataFrame index and returns a colour for it csize (int) – the base size of the circles alpha (float) – transparency of the circles, between 0 and 1 included sizescale (None, pandas.Series) – a Series or dictionary with the same elements as the Index of data, whose values are the size factors that are multiplied to csize. If None, the size of the circles is equal to csize order (None, iterable) – iterable with the elements of data Index, to specify the order in which the circles must be plotted. If None, the order is the same as data.index linewidths (float) – width of the circle line edgecolor (str) – color of the circle line the return value of matplotlib scatter PathCollection

Note

To not have circle lines, edgecolor must be ‘none’ and linewidths equal 0

mgkit.plots.abund.draw_triangle_grid(ax, labels=['LAM', 'SAM', 'EAM'], linewidth=1.0, styles=['-', ':', '--'], fontsize=22)

Changed in version 0.2.0: reworked internals and changed defaults

Draws a triangle as axes, for a planar-simplex projection.

Parameters: ax – an axis instance labels (iterable) – list of string to be put for the axes styles (None, iterable) – either None for solid lines or matplotlib line markers. These are in sync between the internal lines and the axes. linewidth (float) – line width for the axes, the internal lines are equal to 0.75 * linewidth fontsize (float) – font size for the labels, the tick font size is equal to 0.75 * fontsize
mgkit.plots.abund.project_point(point)

Project a tuple containing coordinates (i.e. x, y, z) to planar-simplex.

Parameters: point (tuple) – contains the three coordinates to project the projected point in a planar-simplex tuple