metaseq.plotutils.imshow

metaseq.plotutils.imshow(arr, x=None, ax=None, vmin=None, vmax=None, percentile=True, strip=False, features=None, conf=0.95, sort_by=None, line_kwargs=None, fill_kwargs=None, imshow_kwargs=None, figsize=(5, 12), width_ratios=(4, 1), height_ratios=(4, 1), subplot_params={'wspace': 0.1, 'hspace': 0.1}, subset_by=None, subset_order=None)

Do-it-all function to help with plotting heatmaps

Parameters:

arr : array-like

x : 1D array

X values to use. If None, use range(arr.shape[1])

ax : matplotlib.Axes

If not None, then only plot the array on the provided axes. This will ignore any additional arguments provided that apply to figure-level configuration or to the average line plot. For example, figsize, width_ratios, height_ratios, subplot_params, line_kwargs, and fill_kwargs will all be ignored.

vmin, vmax : float

percentile : bool

If True, then treat values for vmin and vmax as percentiles rather than absolute values.

strip : bool

Include a strip plot alongside the array

features : pybedtools.BedTool or string filename

Features used to construct the array

conf : float

Confidence interval to use in line plot.

sort_by : array-like

Use the provided array to sort the array (e.g., an array of expression values). This array will be argsorted to get the proper order.

line_kwargs, fill_kwargs : dict

Passed directly to ci_plot.

figsize : tuple

(Width, height) of the figure to create.

imshow_kwargs : dict

Passed directly to matplotlib.pyplot.imshow. By default, arguments used are origin=’lower’, aspect=”auto” and a colormap from colormap_adjust.smart_colormap generated using the provided vmin and vmax.

width_ratios, height_ratios: tuple

These tuples are passed to the new_shell function. The default values set up a 2x2 configuration of panels for heatmap, line plot, colorbar axes, and optional strip plot. However modifying width_ratios or height_ratios can be used to create more or fewer panels.

subplot_params : dict

Passed to Figure.subplots_adjust

subset_by : array

An array of any type (but usually int or str) that contains a class label for each row in the heatmap array. For example, to subset by expression, an array the values of “up”, “down”, or “unchanged” at each of the positions could be provided.

Note that the heatmap array is first sorted by sort_by and then split into groups according to subset_by, so each subset remains sorted by sort_by.

subset_order : list-like

This provides the order in which the subsets are plotted. Since the default imshow arguments contain origin=”lower”, these will be plotted in order starting at the bottom of the heatmap.