currentscape.plotting

Plotting-related functions.

Functions

adjust(adjust_left, adjust_right, ...)

Adjust Subplots.

apply_labels_ticks_and_lims(ax, c, xticks, ...)

Apply labels, ticks, xlim and ylim to current / ion concentration plots.

black_line_log_scale(ax, ylim, xlim, ...)

Produce a black line meant to distinguish between 2 plots in log scales.

configure_mpl_rcParams(c)

Configure matplotlib rcParams.

get_colormap(cmap, n_colors, use_patterns, ...)

Get colormap according to input, and add black then white colors at the end.

get_colors(cmap, n_col)

Get colors from colormap, depending on maximum number of colors.

get_colors_hatches_lines_lists(c, curr_idxs, ...)

Get colors and hatches and lines lists from color indexes list.

get_rows_tot(c, ions)

Return the total number of rows cumulated by all the subplots.

plot_x_labels(ax, c, xticks)

Plot x labels and x ticklabels.

remove_ticks_and_frame(ax)

Remove ticks (but not ytick label) and frame.

remove_ticks_and_frame_for_bar_plot(ax)

Remove all ticks (including ytick label) and top & bottom frames.

save_figure(fig, c)

Save figure in output according to config file.

select_color(cmap, i, N_col)

Select color of the ith element when not using patterns.

set_label(ax, x, y, label, textsize)

Set text as label on the y axis.

show_xgridlines(ax, c, xticks[, ylim])

Show vertical gridlines corresponding to the x ticks.

stackplot_with_bars(ax, cnorm, inames, cmap, ...)

Plot currentscape using bars instead of imshow.

stackplot_with_fill_between(ax, cnorm, ...)

Plot currentscape using fill_between.
currentscape.plotting.adjust(adjust_left, adjust_right, adjust_top, adjust_bottom)[source]

Adjust Subplots.

Parameters:

  • adjust_left (float or None) – position of the left edge of the subplots, None to use matplotlib default

  • adjust_right (float or None) – position of the right edge of the subplots, None ot use matplotlib default

  • adjust_top (float or None) – position of the top edge of the subplots, None to use matplotlib default

  • adjust_bottom (float or None) – position of the bottom edge of the subplots, None to use matplotlib default

currentscape.plotting.apply_labels_ticks_and_lims(ax, c, xticks, xlim, ylim, positive=True, config_key='current')[source]

Apply labels, ticks, xlim and ylim to current / ion concentration plots.

Parameters:

  • ax (matplotlib.axes) – currentscape axis

  • c (dict) – config

  • xticks (list) – tick positions on the x axis

  • xlim (list of 2 floats) – limits of x axis

  • ylim (list of 2 floats) – limits of y axis (can be different from ylim from config)

  • positive (bool) – True for positive data, False for negative data

  • config_key (str) – key for getting data from config. Should be ‘current’ or ‘ions’

currentscape.plotting.black_line_log_scale(ax, ylim, xlim, bl_thickness)[source]

Produce a black line meant to distinguish between 2 plots in log scales.

The black line is plotted at the bottom of the upper plot. This is a trick to avoid frames masking some of the data.

Parameters:

  • ax (matplotlib.axes) – currentscape axis

  • ylim (list of 2 floats) – limits of the y axis

  • xlim (list of 2 floats) – limits of the x axis

  • bl_thickness (float) – thickness of the black line separating the two plots, in percentage of the y axis size

Returns ylim, because the bottom y limit is changing by adding the black line.

currentscape.plotting.configure_mpl_rcParams(c)[source]

Configure matplotlib rcParams.

Parameters:

c (dict) – config

currentscape.plotting.get_colormap(cmap, n_colors, use_patterns, N_curr, N_ion)[source]

Get colormap according to input, and add black then white colors at the end.

The black color is used to create a black line separating currentscapes plots, and the white color is used when there is no data (e.g. no inward or outward current).

Parameters:

  • cmap (str) – colormap name

  • n_colors (int) – number of colors to extract IF use_patterns and n_colors>N_curr

  • use_patterns (bool) – True if currentscape plot uses bars and mixes color and pattern

  • N_curr (int) – number of currents

  • N_ion (int) – number of ion concentrations

currentscape.plotting.get_colors(cmap, n_col)[source]

Get colors from colormap, depending on maximum number of colors.

Parameters:

  • cmap (str) – colormap name

  • n_col (int) – number of colors to extract

Returns:

a list of matplotlib colors launch_warning (bool): True to warn that colormap lacks colors

currentscape.plotting.get_colors_hatches_lines_lists(c, curr_idxs, cmap, mapper=None)[source]

Get colors and hatches and lines lists from color indexes list.

Parameters:

  • c (dict) – config

  • curr_idxs (ndarray of ints or int) – list of indexes of currents

  • cmap (matplotlib.colors.Colormap) – colormap

  • mapper (int) – number used to mix colors and patterns

currentscape.plotting.get_rows_tot(c, ions)[source]

Return the total number of rows cumulated by all the subplots.

Parameters:
currentscape.plotting.plot_x_labels(ax, c, xticks)[source]

Plot x labels and x ticklabels.

Parameters:

  • ax (matplotlib.axes) – axis

  • c (dict) – config

  • xticks (list) – tick positions on the x axis

currentscape.plotting.remove_ticks_and_frame(ax)[source]

Remove ticks (but not ytick label) and frame.

Parameters:

ax (matplotlib.axes) – axis

currentscape.plotting.remove_ticks_and_frame_for_bar_plot(ax)[source]

Remove all ticks (including ytick label) and top & bottom frames.

Parameters:

ax (matplotlib.axes) – axis

currentscape.plotting.save_figure(fig, c)[source]

Save figure in output according to config file.

Parameters:

  • fig (matplotlib.figure.Figure) – figure

  • c (dict) – config

currentscape.plotting.select_color(cmap, i, N_col)[source]

Select color of the ith element when not using patterns.

There is a +2 in the formula to account for the black and white in colormap.

Parameters:

  • cmap (matplotlib.colors.Colormap) – colormap

  • i (int) – index of element (current/ion)

  • N_col (int) – total number of elements

currentscape.plotting.set_label(ax, x, y, label, textsize)[source]

Set text as label on the y axis.

Parameters:

  • ax (matplotlib.axes) – axis

  • x (float) – x position of the label

  • y (float) – y position of the label

  • label (str) – text to be displayed as label

  • textsize (int) – text size in pixels

currentscape.plotting.show_xgridlines(ax, c, xticks, ylim=None)[source]

Show vertical gridlines corresponding to the x ticks.

Parameters:

  • ax (matplotlib.axes) – axis

  • c (dict) – config

  • xticks (list) – tick positions on the x axis

  • ylim (list of 2 floats) – limits of y axis

currentscape.plotting.stackplot_with_bars(ax, cnorm, inames, cmap, c, N_curr, mapper=None, top_to_bottom=True)[source]

Plot currentscape using bars instead of imshow.

That way, hatches (patterns) can be used.

Parameters:

  • ax (matplotlib.axes) – currentscape axis

  • cnorm (DataSet) – object containing data (e.g. currents data and idxs)

  • inames (ndarray of ints) – indexes to new name order (new_names = names[inames])

  • cmap (matplotlib.colors.Colormap) – colormap

  • c (dict) – config

  • N_curr (int) – total number of currents

  • mapper (int) – number used to mix colors and patterns

  • top_to_bottom (bool) – if True, plot from top to bottom. if False, plot from bottom to top

Returns the size modified by sum chunks (reduced x resolution)

currentscape.plotting.stackplot_with_fill_between(ax, cnorm, inames, cmap, c, N_curr, mapper=None, top_to_bottom=True)[source]

Plot currentscape using fill_between.

Parameters:

  • ax (matplotlib.axes) – currentscape axis

  • cnorm (DataSet) – object containing data (e.g. currents data and idxs)

  • inames (ndarray of ints) – indexes to new name order (new_names = names[inames])

  • cmap (matplotlib.colors.Colormap) – colormap

  • c (dict) – config

  • N_curr (int) – total number of currents

  • mapper (int) – number used to mix colors and patterns

  • top_to_bottom (bool) – if True, plot from top to bottom. if False, plot from bottom to top