FIGURES Module

This module contains a series of functions to make plots of various nature.

klassez.figures.ax1D(ax, ppm, datax, norm=False, xlims=None, ylims=None, c='tab:blue', lw=0.5, X_label='$\\delta\\ $ F1 /ppm', Y_label='Intensity /a.u.', n_xticks=10, n_yticks=10, label=None, fontsize=10)

Makes the figure of a 1D NMR spectrum, placing it in a given figure panel. This allows the making of modular figures.

The plot can be customized in a very flexible manner by setting the function keywords properly.

Parameters:

axmatplotlib.subplot Object

panel where to put the figure

ppm1darray

ppm scale of the spectrum

datax1darray

spectrum to be plotted

normbool

if True, normalizes the intensity to 1.

xlimslist or tuple

Limits for the x-axis. If None, the whole scale is used.

ylimslist or tuple

Limits for the y-axis. If None, the whole scale is used.

cstr

Colour of the line.

lwfloat

linewidth

X_labelstr

text of the x-axis label;

Y_labelstr

text of the y-axis label;

n_xticksint

Number of numbered ticks on the x-axis of the figure

n_yticksint

Number of numbered ticks on the x-axis of the figure

labelstr

label to be put in the legend.

fontsizefloat

Biggest font size in the figure.

Returns:

lineLine2D Object

Line object returned by plt.plot.

klassez.figures.ax2D(ax, ppm_f2, ppm_f1, datax, xlims=None, ylims=None, cmap='Greys_r', c_fac=1.4, lvl=0.1, lw=0.5, X_label='$\\delta\\,$F2 /ppm', Y_label='$\\delta\\,$F1 /ppm', title=None, n_xticks=10, n_yticks=10, fontsize=10)

Makes a 2D contour plot like the one in klassez.figures.figure2D(), but in a specified panel. Allows for the buildup of modular figures. The contours are drawn according to the formula:

cl = contour_start * contour_factor ** np.arange(contour_num)

where contour_start = np.max(data) * lvl, contour_num = 16 and contour_factor = c_fac. Increasing the value of c_fac will decrease the number of contour lines, whereas decreasing the value of c_fac will increase the number of contour lines.

Parameters:

axmatplotlib.Subplot Object

panel where to put the figure

ppm_f21darray

ppm scale of the direct dimension

ppm_f11darray

ppm scale of the indirect dimension

datax2darray

the 2D NMR spectrum to be plotted

xlimstuple

limits for the x-axis (left, right). If None, the whole scale is used.

ylimstuple

limits for the y-axis (left, right). If None, the whole scale is used.

cmapstr

Colormap identifier for the contour (must be in klassez.CM, or better in klassez.CM_2D)

c_facfloat

Contour factor parameter

lvlfloat

relative height with respect to maximum at which the contour are computed

X_labelstr

text of the x-axis label;

Y_labelstr

text of the y-axis label;

lwfloat

linewidth of the contours

cmapnegstr or None

Colormap identifier for the negative contour. If None, they are not computed at all

n_xticksint

Number of numbered ticks on the x-axis of the figure

n_yticksint

Number of numbered ticks on the x-axis of the figure

fontsizefloat

Biggest font size in the figure.

Returns:

cntmatplotlib.QuadContour object

Drawn contour lines

See also

klassez.figures.figure2D()

klassez.figures.ax_diffplot(axd, axy, ppm, spectrum, dic, color='tab:blue', fmt='o', ms=8, X_label='$\\delta\\,$ F1 /ppm')

Makes a plot of the diffusion coefficients, with error bars, as a function of the integrated regions.

Parameters:

axdmatplotlib.Subplot Object

Subplot for the plot of the diffusion coefficients

axymatplotlib.Subplot Object or None

Subplot for the plot of the spectra. If None, it is not drawn.

ppm1darray

ppm scale of the fitted DOSY spectrum

spectrum2darray

DOSY spectrum

diclist of dict

Dictionary that comes from the klassez.fit.DosyFit class, i.e. from reading a .dy file.

colorstr

Color for the markers that identify the diffusion coefficient

fmtstr

Marker used

msint

Marker size

X_labelstr

Label for the chemical shift axis

Returns:

None

See also

klassez.fit.read_dy()

klassez.fit.DosyFit

klassez.figures.ax_heatmap(ax, data, zlim='auto', z_sym=True, cmap=None, xscale=None, yscale=None, rev=(False, False), n_xticks=10, n_yticks=10, n_zticks=10, fontsize=10)

Computes a heatmap of data on the given ax.

Parameters:

axmatplotlib.Subplot object

Panel where to draw the heatmap

data2darray

Input data

zlimtuple or ‘auto’ or ‘abs’

Vertical limits of the heatmap, that determines the extent of the colorbar. 'auto' means (min(data), max(data)), 'abs' means (min(|data|), max(|data|)).

z_symbool

True to symmetrize the vertical scale around 0.

cmapmatplotlib.cm object

Colormap of the heatmap.

xscale1darray or None

x-scale. None means np.arange(data.shape[1])

yscale1darray or None

y-scale. None means np.arange(data.shape[0])

revtuple of bool

Reverse scale (x, y).

n_xticksint

Number of ticks of the x axis

n_yticksint

Number of ticks of the y axis

n_zticksint

Number of ticks of the color bar

fontsizefloat

Biggest font size to apply to the figure according to klassez.misc.set_fontsizes()

Returns:

immatplotlib.AxesImage

The heatmap

caxmatplotlib.Subplot object

figure panel where the colorbar is drawn

klassez.figures.diffplot(ppm, spectrum, dic, xlims=None, color='tab:blue', X_label='$\\delta\\,$ F1 /ppm', filename=None, ext='svg', dpi=300, dim=None)

Makes a plot of the diffusion coefficients, with error bars, as a function of the integrated regions.

Parameters:

ppm1darray

ppm scale of the fitted DOSY spectrum

spectrum2darray

DOSY spectrum

diclist of dict

Dictionary that comes from the klassez.fit.DosyFit class, i.e. from reading a .dy file.

xlimssequence of float or False or None

Limits for the chemical shift axis. If False, the whole spectrum is plotted. If None, a restricted portion of the spectrum which includes all the fitted regions is shown instead

X_labelstr

Label for the chemical shift axis

filenamestr or None

Filename for the figure to save. If None, the plot is shown instead

extstr

Format for the figure to save

dpiint

Resolution of the figure in dots per inches

dimtuple of int

Dimension of the figure in inches

Returns:

None

See also

klassez.fit.read_dy()

klassez.fit.DosyFit

klassez.figures.dotmd(ppmscale, S, labels=None, lw=0.8, n_xticks=10, rev=True)

Interactive display of multiple 1D spectra.

Parameters:

ppmscale1darray or list of 1darray

ppm scale of the spectra. If only one scale is supplied, all the spectra are plotted using the same scale. Otherwise, each spectrum is plotted using its scale.

Slist of 1darray

spectra to be plotted

labelslist

labels to be put in the legend.

lwfloat

Linewidth of the spectra plots

n_xticksint

Number of numbered ticks on the x-axis of the figure

revbool

When True, the x-scale goes from maximum (left) to minimum (right)

Returns:

scale_factor: list

Intensity of the spectra with respect to the original when the figure is closed

klassez.figures.dotmd_2D(ppm_f1, ppm_f2, S0, labels=None, name='dotmd_2D', X_label='$\\delta\\ $ F2 /ppm', Y_label='$\\delta\\ $ F1 /ppm', n_xticks=10, n_yticks=10, Neg=False)

Interactive display of multiple 2D spectra.

Parameters:

ppm_f11darray

ppm scale of the indirect dimension. If only one scale is supplied, all the spectra are plotted using the same scale. Otherwise, each spectrum is plotted using its scale. There is a 1:1 correspondance between ppm_f1 and S.

ppm_f21darray

ppm scale of the direct dimension. If only one scale is supplied, all the spectra are plotted using the same scale. Otherwise, each spectrum is plotted using its scale. There is a 1:1 correspondance between ppm_f2 and S.

Slist

spectra to be plotted

labelslist

labels to be put in the legend.

namestr

If you choose to save the figure, this is its filename.

X_labelstr

text of the x-axis label;

Y_labelstr

text of the y-axis label;

n_xticksint

Number of numbered ticks on the x-axis of the figure

n_yticksint

Number of numbered ticks on the x-axis of the figure

Negbool

If True, show the negative contours.

Returns:

lvllist

Start of level curves of all the spectra when the figure is closed

klassez.figures.draw_bare_contour(ax, xscale, yscale, data, lvl, cmap='Greys_r', c_fac=1.4, c_num=16, lw=0.5)

Typically used within other functions, this calculates the contour lines and draws them on a given subplot.

Parameters:

axmatplotlib.Subplot Object

Panel where to draw the contours

xscale1darray

X-scale of the contours

yscale1darray

Y-scale of the contours

data2darray

Data where to extract the contour levels from

lvlfloat

Relative height with respect to data for the first contour

c_facfloat

Spacing between next contour lines

c_numint

Number of contour lines to compute

lwfloat

Linewidths for the contours

cmapstr

Colormap identifier for the contour (must be in klassez.CM, or better in klassez.CM_2D)

Returns:

cntmatplotlib.contour.QuadContourSet object

Contour levels set

klassez.figures.figure1D(ppm, datax, norm=False, xlims=None, ylims=None, c='tab:blue', lw=0.5, X_label='$\\delta\\ $ F1 /ppm', Y_label='Intensity /a.u.', n_xticks=10, n_yticks=10, fontsize=10, name=None, ext='svg', dpi=600)

Makes the figure of a 1D NMR spectrum.

The plot can be customized in a very flexible manner by setting the function keywords properly.

Parameters:

ppm1darray

ppm scale of the spectrum

datax1darray

spectrum to be plotted

normbool

if True, normalizes the intensity to 1.

xlimslist or tuple

Limits for the x-axis. If None, the whole scale is used.

ylimslist or tuple

Limits for the y-axis. If None, the whole scale is used.

cstr

Colour of the line.

lwfloat

linewidth

X_labelstr

text of the x-axis label;

Y_labelstr

text of the y-axis label;

n_xticksint

Number of numbered ticks on the x-axis of the figure

n_yticksint

Number of numbered ticks on the x-axis of the figure

fontsizefloat

Biggest font size in the figure.

namestr or None

Filename for the figure to be saved. If None, the figure is shown instead.

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

klassez.figures.figure1D_multi(ppm0, data0, xlims=None, ylims=None, norm=False, c=None, lw=0.5, X_label='$\\delta\\ $ F1 /ppm', Y_label='Intensity /a.u.', n_xticks=10, n_yticks=10, fontsize=10, labels=None, name=None, ext='svg', dpi=600)

Creates the superimposed plot of a series of 1D NMR spectra.

Parameters:

ppm0sequence of 1darray or 1darray

ppm scale of the spectra. If only one scale is supplied, it is assumed to be the same for all the spectra

data0sequence of 1darray

List containing the spectra to be plotted

xlimstuple or None

Limits for the x-axis. If None, the whole scale is used.

ylimstuple or None

Limits for the y-axis. If None, they are automatically set.

normFalse or float or str

If it is False, it does nothing. If it is float, divides all spectra for that number. If it is str(‘#’), normalizes all the spectra to the ‘#’ spectrum (python numbering). If it is whatever else string, normalizes all spectra to themselves.

ctuple or None

List of the colors to use for the traces. None uses the default ones.

lwfloat

Linewidth thickness

X_labelstr

text of the x-axis label

Y_labelstr

text of the y-axis label

n_xticksint

Number of numbered ticks on the x-axis of the figure

n_yticksint

Number of numbered ticks on the x-axis of the figure

fontsizefloat

Biggest fontsize in the picture

labelslist or None or False

List of the labels to be shown in the legend. If it is None, the default entries are used (i.e., ‘1, 2, 3,…’). If it is False, the legend is not shown.

namestr or None

Filename of the figure, if it has to be saved. If it is None, the figure is shown instead.

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

klassez.figures.figure2D(ppm_f2, ppm_f1, datax, xlims=None, ylims=None, cmap='Greys_r', c_fac=1.4, lvl=0.09, X_label='$\\delta\\ $ F2 /ppm', Y_label='$\\delta\\ $ F1 /ppm', lw=0.5, cmapneg=None, n_xticks=10, n_yticks=10, fontsize=10, name=None, ext='svg', dpi=600)

Makes a 2D contour plot. The contours are drawn according to the formula:

cl = contour_start * contour_factor ** np.arange(contour_num)

where contour_start = np.max(data) * lvl, contour_num = 16 and contour_factor = c_fac. Increasing the value of c_fac will decrease the number of contour lines, whereas decreasing the value of c_fac will increase the number of contour lines.

Parameters:

ppm_f21darray

ppm scale of the direct dimension

ppm_f11darray

ppm scale of the indirect dimension

datax2darray

the 2D NMR spectrum to be plotted

xlimstuple

limits for the x-axis (left, right). If None, the whole scale is used.

ylimstuple

limits for the y-axis (left, right). If None, the whole scale is used.

cmapstr

Colormap identifier for the contour (must be in klassez.CM, or better in klassez.CM_2D)

c_fac: float

Contour factor parameter

lvlfloat

relative height with respect to maximum at which the contour are computed

X_labelstr

text of the x-axis label;

Y_labelstr

text of the y-axis label;

lwfloat

linewidth of the contours

cmapnegstr or None

Colormap identifier for the negative contour. If None, they are not computed at all

n_xticksint

Number of numbered ticks on the x-axis of the figure

n_yticksint

Number of numbered ticks on the x-axis of the figure

fontsizefloat

Biggest font size in the figure.

namestr

Filename for the figure

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

Returns:

None

See also

klassez.figures.ax2D()

klassez.figures.figure2D_multi(ppm_f2, ppm_f1, datax, xlims=None, ylims=None, lvl='default', c_fac=1.4, Negatives=False, X_label='$\\delta\\ $ F2 /ppm', Y_label='$\\delta\\ $ F1 /ppm', lw=0.5, n_xticks=10, n_yticks=10, labels=None, name=None, ext='svg', dpi=600)

Generates the figure of multiple, superimposed spectra, using klassez.figures.ax2D().

Parameters:

ppm_f21darray

ppm scale of the direct dimension

ppm_f11darray

ppm scale of the indirect dimension

dataxsequence of 2darray

the 2D NMR spectra to be plotted

xlimstuple

limits for the x-axis (left, right). If None, the whole scale is used.

ylimstuple

limits for the y-axis (left, right). If None, the whole scale is used.

lvl“default” or list

height with respect to maximum at which the contour are computed. If “default”, each spectrum is at 10% of maximum height. Otherwise, each entry of the list corresponds to the contour height of the respective spectrum.

c_facfloat

Contour factor

Negativesbool

set it to True if you want to see the negative part of the spectrum

X_labelstr

text of the x-axis label;

Y_labelstr

text of the y-axis label;

lwfloat

linewidth of the contours

n_xticksint

Number of numbered ticks on the x-axis of the figure

n_yticksint

Number of numbered ticks on the x-axis of the figure

labelslist

entries of the legend. If None, the spectra are numbered.

namestr

Filename for the figure. If None, it is shown instead of saved

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

Returns:

None

See also

klassez.figures.ax2D()

klassez.figures.heatmap(data, zlim='auto', z_sym=True, cmap=None, xscale=None, yscale=None, rev=(False, False), n_xticks=10, n_yticks=10, n_zticks=10, fontsize=10, filename=None, ext='svg', dpi=300)

Computes a heatmap of data.

Parameters:

data: 2darray

Input data

zlim: tuple or ‘auto’ or ‘abs’

Vertical limits of the heatmap, that determines the extent of the colorbar. 'auto' means (min(data), max(data)), 'abs' means (min(|data|), max(|data|)).

z_sym: bool

True to symmetrize the vertical scale around 0.

cmap: matplotlib.cm object

Colormap of the heatmap.

xscale: 1darray or None

x-scale. None means np.arange(data.shape[1])

yscale: 1darray or None

y-scale. None means np.arange(data.shape[0])

rev: tuple of bool

Reverse scale (x, y).

n_xticks: int

Number of ticks of the x axis

n_yticks: int

Number of ticks of the y axis

n_zticks: int

Number of ticks of the color bar

fontsize: float

Biggest font size to apply to the figure according to klassez.misc.set_fontsizes()

filename: str or None

Filename for the figure. Set to None to show the figure.

extstr

Figure format to be saved.

dpiint

Resolution of the figure to be saved in dots per inches

Returns:

None

See also

klassez.figures.ax_heatmap()

klassez.figures.ongoing_fit(exp, calc, residual, ylims=None, filename=None, ext='svg', dpi=100)

Makes a figure of an ongoing fit. It displays the experimental data and the model, and the residuals in a separate window. The figure can be either saved or shown.

Tip

This function has been designed to be fast at rendering! If you want to save it, use ext='svg' and low dpi otherwise the writing time to disk becomes too slow.

Parameters:

exp1darray

Experimental data

calc1darray

Current model

residual1darray

Residuals of the fit

ylimstuple

Optional limits for y-axis

filenamestr or None

Filename of the figure to be saved. If None, the figure is shown instead

dpiint

Resolution of the figure in dots per inches

klassez.figures.plot_1D(x, y, SFO1, name='Spectrum', X_label='$\\delta\\,$ /ppm')

Plots the real part of the spectrum in an interactive panel for inspection.

Parameters:

x1darray

PPM (or frequency) scale

y1darray

Spectrum

SFO1float

Nucleus Larmor frequency

namestr

Title for the figure

X_labelstr

Label for the x axis.

Returns:

None

klassez.figures.plot_2D(x_f1, x_f2, yy, SFO1=1, SFO2=1, Neg=True, lvl0=0.2, name='Spectrum', X_label='$\\delta\\,$F2 /ppm', Y_label='$\\delta\\,$F1 /ppm')

Plots the real part of the spectrum. Use the mouse scroll to adjust the contour starting level.

Parameters:

x_f11darray

PPM (or frequency) scale for the y axis

x_f21darray

PPM (or frequency) scale for the x axis

yy2darray

Spectrum

SFO1float

Nucleus Larmor frequency of the indirect dimension

SFO2float

Nucleus Larmor frequency of the direct dimension

Negbool

Display also the negative part of the spectrum

lvl0float

Starting contour level, with respect to the maximum of the spectrum

namestr

Filename for the figure.

X_labelstr

Label for the x axis.

Y_labelstr

Label for the y axis.

Returns:

None

klassez.figures.plot_fid(fid, name=None, ext='svg', dpi=600)

Makes a two-panel figure that shows on the left the real part of the FID, on the right the imaginary part. The x-scale and y-scale are automatically adjusted.

Parameters:

fidndarray

FID to be plotted

namestr

Name of the figure

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

klassez.figures.plot_fid_re(fid, scale=None, c='b', lims=None, name=None, ext='svg', dpi=600)

Makes a single-panel figure that shows either the real or the imaginary part of the FID. The x-scale and y-scale are automatically adjusted.

Parameters:

fidndarray

FID to be plotted

scale1darray or None

x-scale of the figure

cstr

Color

limstuple or None

Limits

namestr

Name of the figure

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

klassez.figures.plot_p3D(x_f1, x_f2, idx_scale, yyy, dim='31', Neg=True, lvl0=0.2, name='', X_label='$\\delta\\,$ /ppm', Y_label='')

Plots the real part of the spectrum. Use the mouse scroll to adjust the contour starting level. Use the ‘<<’ and ‘>>’ to move across planes.

Parameters:

x_f11darray

PPM (or frequency) scale for the y axis

x_f21darray

PPM (or frequency) scale for the x axis

idx_scale1darray

Scale for the non-directly plotted dimension

yyy3darray

Spectrum

dimstr

Slicing direction.

• dim = '31' –> Plot planes F3-F1 –> idx_scale represent F2

• dim = '32' –> Plot planes F3-F2 –> idx_scale represent F1

Negbool

Display also the negative part of the spectrum

lvl0float

Starting contour level, with respect to the maximum of the spectrum

namestr

Filename for the figure.

X_labelstr

Label for the x axis.

Y_labelstr

Label for the y axis.

Returns:

None

klassez.figures.redraw_contours(ax, ppm_f2, ppm_f1, S, lvl, cnt, Neg=False, Ncnt=None, cmap=[None, None], c_fac=1.4, c_num=16, lw=0.5)

Redraws the contours in interactive 2D visualizations.

Parameters:

axmatplotlib.Subplot Object

Panel of the figure where to draw the contours

ppm_f21darray

ppm scale of the direct dimension

ppm_f11darray

ppm scale of the indirect dimension

S2darray

Spectrum

lvlfloat

Level at which to draw the contours

cntmatplotlib.contour.QuadContourSet object

Pre-existing contours

Negbool

Choose if to draw the negative contours (True) or not (False)

Ncntmatplotlib.contour.QuadContourSet object

Pre-existing negative contours

lwfloat

Linewidth

cmaplist

Colour of the contours. [cmap +, cmap -]

Returns:

cntmatplotlib.contour.QuadContourSet object

Updated contours

Ncntmatplotlib.contour.QuadContourSet object or None

Updated negative contours if Neg is True, None otherwise

See also

klassez.figures.draw_bare_contour()

klassez.figures.sns_heatmap(data, name=None, ext='svg', dpi=600)

Computes a heatmap of data. This function employs the seaborn package. Specify name if you want to save the figure.

Parameters:

data2darray

Data of which to compute the heatmap. Make sure the entries are real numbers.

namestr or None

Filename of the figure to be saved. If None, the figure is shown instead.

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

klassez.figures.stacked_plot(ppmscale, S, xlims=None, lw=0.5, X_label='$\\delta\\ $ F1 /ppm', Y_label='Normalized intensity /a.u.', n_xticks=10, labels=None, name=None, ext='svg', dpi=600)

Creates a stacked plot of all the spectra contained in the list S. Note that S MUST BE a list. All the spectra must share the same scale.

Parameters:

ppmscale1darray

ppm scale of the spectrum

Slist of 1darray

spectra to be plotted

xlimslist or tuple

Limits for the x-axis. If None, the whole scale is used.

lwfloat

linewidth

X_labelstr

text of the x-axis label;

Y_labelstr

text of the y-axis label;

n_xticksint

Number of numbered ticks on the x-axis of the figure

labelslist

labels to be put in the legend.

namestr

filename of the figure, if it has to be saved;

extstr

Format of the image

dpiint

Resolution of the image in dots per inches

Returns:

None

See also

klassez.figures.ax1D()