PlottingFunctions module

Class related to making figure-quality plots.

Probably best to set your default sans-serif font to Helvetica before you make figures: https://fowlerlab.org/2019/01/03/changing-the-sans-serif-font-to-helvetica/

The maximum published width for a one-column figure is 3.33 inches (240 pt). The maximum width for a two-column figure is 6.69 inches (17 cm). The maximum depth of figures should be 8 ¼ in. (21.1 cm).

panel labels are 8 point font, ticks are 7 point font, annotations and legends are 6 point font.

class PlottingFunctions.Plotter(poster=False)

Bases: object

histogram_plot(axs, data, bins, xlim=None, ylim=None, histcolor='gray', xaxislabel='x axis', alpha=1, histtype='bar', density=True)

histogram_plot function takes data and makes a histogram

Parameters:

• data (np.1darray) – data array

• bins (np.1darray) – bin array

• xlim (boolean or list of two floats) – default is None (which computes min/max of x), otherwise provide a min/max

• ylim (boolean or list of two floats) – default is None (which computes min/max of y), otherwise provide a min/max

• histcolor (string) – histogram colour (default is gray)

• xaxislabel (string) – x axis label (default is ‘x axis’)

• alpha (float) – histogram transparency (default 1)

• histtype (string) – histogram type, default bar

• density (boolean) – if to plot as pdf, default True

Returns:

axs (axis) – axis object

image_plot(axs, data, vmin=None, vmax=None, cmap='gist_gray', cbar='on', cbarlabel='photons', label='', labelcolor='white', pixelsize=110, scalebarsize=5000, scalebarlabel='5$\\,\\mu$m', alpha=1, plotmask=False, mask=None)

image_plot function takes image data and makes an image plot

Parameters:

• data (np.2darray) – image

• vmin (float) – minimum pixel intensity displayed (default 0.1%)

• vmax (float) – minimum pixel intensity displayed (default 99.9%)

• cmap (string) – colour map used; default gray)

• cbarlabel (string) – colour bar label; default ‘photons’

• label (string) – is any annotation

• labelcolor (string) – annotation colour

• pixelsize (float) – pixel size in nm for scalebar, default 110

• scalebarsize (float) – scalebarsize in nm, default 5000

• scalebarlabel (string) – scale bar label, default 5 um

Returns:

axs (axis) – axis object

image_scatter_plot(axs, data, xdata, ydata, vmin=None, vmax=None, cmap='gist_gray', cbar='on', cbarlabel='photons', label='', labelcolor='white', pixelsize=110, scalebarsize=5000, scalebarlabel='5$\\,\\mu$m', alpha=1, scattercolor='red', s=20, lws=0.75)

image_plot function takes image data and makes an image plot

Parameters:

• data (np.2darray) – image

• xdata (np.1darray) – scatter points, x

• ydata (np.1darray) – scatter points, y

• vmin (float) – minimum pixel intensity displayed (default 0.1%)

• vmax (float) – minimum pixel intensity displayed (default 99.9%)

• cmap (string) – colour map used; default gray)

• cbarlabel (string) – colour bar label; default ‘photons’

• label (string) – is any annotation

• labelcolor (string) – annotation colour

• pixelsize (float) – pixel size in nm for scalebar, default 110

• scalebarsize (float) – scalebarsize in nm, default 5000

• scalebarlabel (string) – scale bar label, default 5 um

Returns:

axs (axis) – axis object

two_column_plot(nrows=1, ncolumns=1, heightratio=[1], widthratio=[1], height=0, big=False)

two_column_plot function takes data and makes a two-column width figure

Parameters:

• nrows (int) – number of rows

• ncolumns (int) – number of columns

• heightratio (list) – list of heights of same length as nrows

• widthratio (list) – list of widths of same length as ncolumns

• height (float) – overridden height of figure

• big (boolean) – if big is True, uses larger font sizes

Returns:

• fig (figure) – figure object

• ax (axes) – axes object