unidec.modules.plotting package

Submodules

unidec.modules.plotting.ColorPlot module

class unidec.modules.plotting.ColorPlot.ColorPlot2D(*args, **kwargs)

Bases: PlottingWindowBase

Method to perform a 3D plot by plotting the Z axis as 2D slices of a different color. Each 2D slice uses the alpha (trasparency) parameter to indicate intensity in square root scale.

make_color_plot(mzgrid, mzax, dtax, ztab)

Creates the color plot :param mzgrid: mz x dt x z numpy array of intensity values :param mzax: m/z axis :param dtax: drift time axis :param ztab: charge axis :return: None

make_compare_color_plot(data1, data2, test_kda=True, xlab='', ylab='')

unidec.modules.plotting.NoZoomSpan module

class unidec.modules.plotting.NoZoomSpan.NoZoomSpan(axes, onselect, parent=None, minspan=None, useblit=False, rectprops=None, zoombutton=None, onmove_callback=None)

Bases: ZoomCommon

Expansion of matplotlib embed in wx example by John Bender and Edward Abraham, see https://www.scipy.org/Matplotlib_figure_in_a_wx_panel

This version allows the user to zoom in on the figure using either a span selector or a box selector. You can also set a persistent span selector that acts as cursor references on top of whatever is plotted

ZoomSpan based on matplotlib.widgets.SpanSelector CursorSpan based on matplotlib.widgets.SpanSelector BoxZoom based on matplotlib.widgets.RectangleSelector

Brian J. Soher, Duke University, 20 October, 2010

Select a min/max range of the x or y axes for a matplotlib Axes

Example usage:

axes = subplot(111) axes.plot(x,y)

def onselect(vmin, vmax):

print vmin, vmax

span = ZoomSpan(axes, onselect, ‘horizontal’)

onmove_callback is an optional callback that will be called on mouse move with the span range

ignore(event)

return True if event should be ignored

new_axes(axes)
onmove(event)
press(event)

on button press event

release(event)

on button release event

update()

draw using newfangled blit or oldfangled draw depending on useblit

update_background(event)

force an update of the background

unidec.modules.plotting.PlotAnimations module

class unidec.modules.plotting.PlotAnimations.AnimationWindow(parent, data_list, config=None, yvals=None, mode='1D', pks=None, pksmode='mz', *args, **kwargs)

Bases: Frame

add_peaks(e=None)
add_peaks_mass(e=None)
add_peaks_mz(e=None)
init()

Create a fresh plot and start the animation. :return: None

on_back(e)

Plot the previous data set in data_list. :param e: Unused event :return: None

on_close(e)

Stop the animation and close the window. :param e: Unused event :return: None

on_next(e)

Plot the next data set in data_list. :param e: Unused event :return: None

on_play(e)

Toggles self.play on or off. Will break the while loop in self.update if self.play = False. :param e: Unused event :return: None

on_save_fig(e=None)
refresh_plot()

Create a fresh plot from the top. :return: None

save_fig(base, ext)
update(frame_number)

Continues to increment the plot to the next value in the data_list. Will stop if self.play is False. :param frame_number: Required but unused. Filled by FuncAnimation. :return: 0

update_framerate(e)

Change the frame rate. Restart the animation with fresh frame rate. :param e: Unused event :return: None

update_plot()

Increment to the next data set and update the plot with the new data. Tries to keep some of the old plotting parameters like the zoom the same. Stops the animation if an error occurs. :return: None

unidec.modules.plotting.PlotBase module

class unidec.modules.plotting.PlotBase.PlotBase(*args, **kwargs)

Bases: object

Class for matplotlib plots

add_legend(location=1, anchor=None)

Adds a legend to the plot. :param location: Integer code for location :param anchor: BBox to anchor parameter :return: None

add_rect(xstart, ystart, xwidth, ywidth, alpha=0.5, facecolor='k', edgecolor='k', nopaint=False)
add_title(title='')
addtext(txt, x, y, vlines=True, hlines=False, color='k', ymin=0, ymax=None, verticalalignment='top', xmin=0, xmax=None, nopaint=False, **kwargs)

Adds text and lines. Puts things that have been added in self.lines and self.text lists. :param txt: String of text to add :param x: x position for where to add :param y: y position for where to add :param vlines: Whether to add vertical lines to the text as well. :param hlines: Whether to add horizontal lines to the text as well. :param color: Color of text and lines :param ymin: Minimum value of vlines :param ymax: Maximum value of vlines :param verticalalignment: Vertical alignment of the text :param xmin: Minimum value of hlines :param xmax: Maximum value of hlines :param nopaint: Don’t paint it :param kwargs: Keywords If range=(a,b) is specified, adds a line from a to b and vertical lines at a and b. :return: None

clear_plot(*args)

Clear the plot and rest some of the parameters. :param args: Arguments :return:

draw_mz_curve(sarray, color='y', alpha=0.4, adduct_mass=1, repaint=False)
get_blank_axis(scale=None)
get_limits()
get_linewidth()
get_png()

Returns PNG string of figure. :return: PNG string

get_svg()

Returns SVG string of figure. :return: SVG string

get_zoomvals()
kda_test(xvals)

Test whether the axis should be normalized to convert mass units from Da to kDa. Will use kDa if: xvals[int(len(xvals) / 2)] > 100000 or xvals[len(xvals) - 1] > 1000000

If kDa is used, self.kda=True and self.kdnorm=1000. Otherwise, self.kda=False and self.kdnorm=1. :param xvals: mass axis :return: None

on_save_fig(evt, path, **kwargs)

Save figure to path. :param evt: wx.Event (unused) :param path: Path to save figure to :param kwargs: keywords passed to save_figure :return: None

plotadddot(x, y, colval, markval, label='', linewidth=None)

Adds a scatter plot to the figure. May be one or more. :param x: x values :param y: y values :param colval: Color :param markval: Marker :param label: Label for Plot :param linewidth: Line width :return: None

repaint(setupzoom=False, resetzoom=False)
reset_zoom()
save_figure(path, **kwargs)

Saves Figure to path. :param path: Path to save figure at. :param kwargs: Keywords passed to matplotlib.figure.savefig (note only specific ones are passed) :return: None

set_aspect(aspect=None)
set_color(rgbtuple=None)

Sets background color :param rgbtuple: background color :return:

set_nticks(bins)

Set the number of ticks in the x-axis. :param bins: Number of ticks in the x-axis :return: None

set_tickcolor()

Sets tick colors based on the colormap set at self.cmap :return: None

set_zoomvals(zoomvals=None)
setup_zoom(plots=None, zoom=None, data_lims=None, pad=0, groups=None)
textremove()

Remove text and lines previous placed in the self.text and self.lines containers :return: None

update_style(stylefile=None)
write_data(path)
zoomout()

unidec.modules.plotting.PlottingWindow module

class unidec.modules.plotting.PlottingWindow.MZLimitsEvent(evttype, id, minval=None, maxval=None)

Bases: PyCommandEvent

class unidec.modules.plotting.PlottingWindow.NetworkFrame(*args, **kwargs)

Bases: PlottingWindowBase

clear_frame()
class unidec.modules.plotting.PlottingWindow.Plot1d(*args, **kwargs)

Bases: PlottingWindowBase, Plot1dBase

Class for 1D plots.

class unidec.modules.plotting.PlottingWindow.Plot2d(*args, **kwargs)

Bases: PlottingWindowBase, Plot2dBase

Plotting class for 2D contour plots

class unidec.modules.plotting.PlottingWindow.PlotAny(*args, **kwargs)

Bases: PlottingWindowBase, Plot1dBase, Plot2dBase

Plotting class for 2D contour plots

class unidec.modules.plotting.PlottingWindow.PlottingWindowBase(*args, **kwargs)

Bases: PlotBase, Panel

Class for wx window with embedded matplotlib plots Inherits from PlotBase, which is the core functions stripped of everything interactive

copy_to_clipboard(*args, **kwargs)
mouse_activate(event)
mouse_inactivate(event)
on_draw(event)
on_idle(event)

Function triggered on idle event from plot. :param event: wx.Event :return: None

on_key(evt)
on_left_click(x, y)
on_newxy(x, y)
on_release(event)

Function triggered on button release event from plot. Currently wired to trigger on_save_figure_dialog on middle button. :param event: wx.Event :return: None

on_right_click(event=None)
on_save_fig(evt, path, **kwargs)

Save figure to path. :param evt: wx.Event (unused) :param path: Path to save figure to :param kwargs: keywords passed to save_figure :return: None

on_save_fig_dialog(evt)

Open a save figure dialog for specified plot. :param evt: wx.Event (unused) :return: None

on_scans_selected(smin, smax)
on_size(event)

Resizes the plots :param event: wx.Event :return: None

on_swoop_drag(sarray)
on_write_dialog(evt)

Open a save figure dialog for specified plot. :param evt: wx.Event (unused) :return: None

repaint(setupzoom=True, resetzoom=False)

Redraw and refresh the plot. :param setupzoom: Boolean, whether to setup zooming :param resetzoom: Boolean, whether to reset zooming :return: None

set_resize(newsize)
setup_zoom(plots, zoom, data_lims=None, pad=0, groups=None)

Set up zoom on axes. :param pad: Padding around plot :param plots: Axes objects to setup :param zoom: Type of zoom (‘span’ or ‘box’) :param data_lims: Optional manual description of the data limits (where to go when fully zoomed out) :param groups: Group of axes to link zoom together for :return: None

size_handler(event=None, *args, **kwargs)

Resizes the plots :param args: :param kwargs: :return: None

zoomout()
class unidec.modules.plotting.PlottingWindow.ScanSelectedEvent(evttype, id, smin=None, smax=None)

Bases: PyCommandEvent

class unidec.modules.plotting.PlottingWindow.SwoopDragEvent(evttype, id, sarray=None)

Bases: PyCommandEvent

unidec.modules.plotting.ZoomBox module

class unidec.modules.plotting.ZoomBox.ZoomBox(axes, onselect, parent=None, groups=None, drawtype='box', minspanx=None, minspany=None, useblit=False, lineprops=None, rectprops=None, onmove_callback=None, spancoords='data', button=None, data_lims=None, swoop=False, integrate=0, smash=0, pad=0.0001)

Bases: ZoomCommon

Select a min/max range of the x axes for a matplotlib Axes

Example usage:

from matplotlib.widgets import  RectangleSelector
from pylab import *

def onselect(xmin, xmax, value, ymin, ymax):
  'eclick and erelease are matplotlib events at press and release'
  print ' x,y min position : (%f, %f)' % (xmin, ymin)
  print ' x,y max position   : (%f, %f)' % (xmax, ymax)
  print ' used button   : ', eclick.button

def toggle_selector(event):
    print ' Key pressed.'
    if event.key in ['Q', 'q'] and toggle_selector.RS.active:
        print ' RectangleSelector deactivated.'
        toggle_selector.RS.set_active(False)
    if event.key in ['A', 'a'] and not toggle_selector.RS.active:
        print ' RectangleSelector activated.'
        toggle_selector.RS.set_active(True)

x = arange(100)/(99.0)
y = sin(x)
fig = figure
axes = subplot(111)
axes.plot(x,y)

toggle_selector.RS = ZoomBox(axes, onselect, drawtype='line')
connect('key_press_event', toggle_selector)
show()
ignore(event)

return True if event should be ignored

initialize()
new_axes(axes, rectprops=None)
onmove(event)
press(event)

on button press event

release(event)

on button release event

set_clipping()
update()

draw using newfangled blit or oldfangled draw depending on useblit

zoomout(event=None)

unidec.modules.plotting.ZoomCommon module

unidec.modules.plotting.ZoomCommon.GetMaxes(axes, xmin=None, xmax=None)
unidec.modules.plotting.ZoomCommon.GetStart(axes)
unidec.modules.plotting.ZoomCommon.ResetVisible(axes)
class unidec.modules.plotting.ZoomCommon.ZoomCommon

Bases: object

get_active()

to get status of active mode (boolean variable)

kill_labels()
label()
left_click(x, y)
on_newxy(x, y)
peakdetect(data, window=10.0, threshold=0.0)
right_click(event=None)
scans_selected(vmin, vmax)
set_active(active)

Use this to activate / deactivate the RectangleSelector

from your program with an boolean variable ‘active’.

set_auto_ylim(xmin, xmax, draw=True)
set_manual(xmin, xmax)
set_manual_y(ymin, ymax)
set_xlim(xmin, xmax, draw=True)
set_ylim(ymin, ymax, draw=True)
switch_label()
update_background(event)

force an update of the background

unidec.modules.plotting.ZoomCommon.clip_all(axes)
unidec.modules.plotting.ZoomCommon.clip_none(axes)
unidec.modules.plotting.ZoomCommon.set_clipping(axes)
unidec.modules.plotting.ZoomCommon.special_clip(axes)

unidec.modules.plotting.ZoomSpan module

class unidec.modules.plotting.ZoomSpan.ZoomSpan(axes, onselect, parent=None, minspan=None, useblit=False, rectprops=None, onmove_callback=None)

Bases: ZoomCommon

Expansion of matplotlib embed in wx example by John Bender and Edward Abraham, see https://www.scipy.org/Matplotlib_figure_in_a_wx_panel

This version allows the user to zoom in on the figure using either a span selector or a box selector. You can also set a persistent span selector that acts as cursor references on top of whatever is plotted

ZoomSpan based on matplotlib.widgets.SpanSelector CursorSpan based on matplotlib.widgets.SpanSelector BoxZoom based on matplotlib.widgets.RectangleSelector

Brian J. Soher, Duke University, 20 October, 2010

Select a min/max range of the x or y axes for a matplotlib Axes

Example usage:

axes = subplot(111) axes.plot(x,y)

def onselect(vmin, vmax):

print vmin, vmax

span = ZoomSpan(axes, onselect, ‘horizontal’)

onmove_callback is an optional callback that will be called on mouse move with the span range

ignore(event)

return True if event should be ignored

new_axes(axes)
onmove(event)
press(event)

on button press event

release(event)

on button release event

update()

draw using newfangled blit or oldfangled draw depending on useblit

zoomout(event=None)

unidec.modules.plotting.plateplot module

class unidec.modules.plotting.plateplot.PlateFrame(parent)

Bases: Frame

change_type(e=None)
draw()
load_eng(eng)
make_plot(data=None)
onmove(e=None)
replot(e=None)
class unidec.modules.plotting.plateplot.PlatePlot(*args, **kwargs)

Bases: PlottingWindowBase

Plotting class for 3D Waterfall plots.

make_plate(type=96)
onmove(e=None)
populate(positions, colors=None)
unidec.modules.plotting.plateplot.cc(arg)

unidec.modules.plotting.plot1d module

class unidec.modules.plotting.plot1d.Plot1dBase(*args, **kwargs)

Bases: PlotBase

add_centroid(centroids, color=None, repaint=True)

Add a centroid line to the plot. :param centroids: Centroid array :param color: Color :param repaint: Boolean, whether to repaint or not :return: None

barplottop(xarr, yarr, peakval, colortab, xlabel='', ylabel='', title='', zoom='box', repaint=True)

Create a bar plot. :param xarr: x value array :param yarr: y value array :param peakval: Bar labels to be listed below bars :param colortab: List of colors for the various bars :param xlabel: Label for x axis :param ylabel: Label for y axis :param title: Plot title :param zoom: Type of zoom (‘box’ or ‘span) :param repaint: Boolean, whether to repaint or not when done. :return: None

barplottoperrors(xarr, yarr, peakval, colortab, xlabel='', ylabel='', title='', zoom='box', repaint=True, xerr=0, yerr=0)

Create a bar plot. :param xarr: x value array :param yarr: y value array :param peakval: Bar labels to be listed below bars :param colortab: List of colors for the various bars :param xlabel: Label for x axis :param ylabel: Label for y axis :param title: Plot title :param zoom: Type of zoom (‘box’ or ‘span) :param repaint: Boolean, whether to repaint or not when done. :param xerr: for error bars :param yerr: for error bars :return: None

centroid_plot(centroids, color=None, xlabel='m/z', ylabel='', title='', zoom='box', repaint=True)

Create a centroid line plot. :param xarr: x value array :param yarr: y value array :param color: List of colors for the various dots :param xlabel: Label for x axis :param ylabel: Label for y axis :param title: Plot title :param zoom: Type of zoom (‘box’ or ‘span) :param repaint: Boolean, whether to repaint or not when done. :return: None

colorplotMD(xvals, yvals, cvals, title='', xlabel='', ylabel='', clabel='Mass Defect', cmap='hsv', config=None, color='black', max=1, marker=None, zoom='box', nopaint=False, test_kda=False, integerticks=False, **kwargs)
errorbars(xvals, yvals, xerr=None, yerr=None, color='black', newlabel='', nopaint=True, **kwargs)
filledplot(x, y, color='black')

Creates a plot filled between the y values and the y axis :param x: x values :param y: y values :param color: color :return: None

histogram(xarray, labels=None, xlab='', ylab='', title='')

Creates a histogram plot. :param xarray: Array of values in (N x M) array :param labels: Labels for value :param xlab: x axis label :param ylab: y axis label :param title: Plot Title :return: None

insetplot(x, y, a, b)
multiplot(x, y, a, b)
plotadd(xvals, yvals, colval='black', newlabel='', nopaint=True, **kwargs)

Adds a plot. :param xvals: x values :param yvals: y values :param colval: Color :param newlabel: Label :param nopaint: Boolean, whether to repaint or not :return: None

plotrefreshtop(xvals, yvals, title='', xlabel='', ylabel='', label='', config=None, color='black', marker=None, zoom='box', nopaint=False, test_kda=False, integerticks=False, zoomout=False, **kwargs)

Create a new 1D plot. :param xvals: x values :param yvals: y values :param title: Plot title :param xlabel: x axis label :param ylabel: y axis label :param label: label for legend :param config: UniDecConfig object :param color: Plot color :param marker: Marker type :param zoom: zoom type (‘box’ or ‘span’) :param nopaint: Boolean, whether to repaint or not :param test_kda: Boolean, whether to attempt to plot kDa rather than Da :param integerticks: Boolean, whether to use inter tickmarks only :param zoomout: Boolean, whether to zoom out :param kwargs: Keywords :return: None

scatterplottop(xarr, yarr, color=None, xlabel='', ylabel='', title='', zoom='box', repaint=True)

Create a bar plot. :param xarr: x value array :param yarr: y value array :param color: List of colors for the various dots :param xlabel: Label for x axis :param ylabel: Label for y axis :param title: Plot title :param zoom: Type of zoom (‘box’ or ‘span) :param repaint: Boolean, whether to repaint or not when done. :return: None

unidec.modules.plotting.plot2d module

class unidec.modules.plotting.plot2d.Plot2dBase(*args, **kwargs)

Bases: PlotBase

Plotting class for 2D contour plots

contourplot(dat=None, config=None, xvals=None, yvals=None, zgrid=None, xlab='m/z (Th)', ylab='Charge', title='', normflag=1, normrange=None, repaint=True, nticks=None, test_kda=False, discrete=None, ticloc=None, ticlab=None, order=None)

Make 2D plot.

Data can be added using two methods:

  1. If dat is specified, it will look for an N x 3 list of x,y,z values

  2. If xvals, yvals, and zgrid are filled, it will plot zgrid assuming its shape is (len(xvals),len(yvals))

Parameters:

  • dat – N x 3 list in [x,y,z] format of data to be plotted

  • config – UniDecConfig object

  • xvals – x-axis values

  • yvals – y-axis values

  • zgrid – numpy array of shape (len(xvals),len(yvals))

  • xlab – Label for x-axis

  • ylab – Label for y-axis

  • title – Plot title

  • normflag – Set to 1 to normalize the plot range from min to max. If 0, will not normalize.

  • normrange – Range to normalize to if normflag is 0.

  • repaint – If true, will repaint the plot after it is done.

  • nticks – Number of ticks on the x-axis. If None, will use default.

  • test_kda – If true, will decide if the x-axis is better displayed in Da or kDa units.

Returns:

None

hist2d(xvals, yvals, bins, config=None, xlab='m/z (Th)', ylab='Charge', title='', repaint=True, nticks=None, test_kda=False)
plot_native_z(offset, col, xvals, width=0, alpha=1, shape=0)

Plots a showing the native charge offsets. :param offset: Offset value :param col: Color :param xvals: x-axis (mass) :param width: Width of charge distribution. :param alpha: Transparency of plot overlay :param shape: Indicates whether the width defines a step function of a Gaussian distribution :return: None

unidec.modules.plotting.plot3d module

class unidec.modules.plotting.plot3d.CubePlot(*args, **kwargs)

Bases: PlottingWindowBase

Plotting class for cube plots. Performs isometric projections of three 2D plots onto three faces of a cube.

cubeplot(xaxis, yaxis, zaxis, C, C2, C3, xlab='', ylab='', zlab='', cmap='jet')

Make 2D isometric projection plot of three cube faces :param xaxis: X-axis values :param yaxis: Y-axis values :param zaxis: Z-axis values :param C: Intensity grid for X v. Y face :param C2: Intensity grid for X v. Z face :param C3: Intensity grid for Y v. Z face :param xlab: X-axis label :param ylab: Y-axis label :param zlab: Z-axis label :param cmap: Colormap for 2D plot :return: None

isogrids()

Sets jsometric projections of X, Y, and Z axis grids :return: None

isolabels(xticlab, yticlab, zticlab, ax, col)

Draw isometric projection of axis labels :param xticlab: X-axis label (string) :param yticlab: Y-axis label (string) :param zticlab: Z-axis label (string) :param ax: Axis object :param col: Color (not presently used) :return: None

isolines()

Draw isometric projection of lines at the edge of the cube. :return: None

isometric_projection(x, y, z)

Give the isometric projection of a given (x,y,z) onto a plane set by self.alpha and self.beta :param x: x value (float) :param y: y value (float) :param z: z value (float) :return: o, isometric projection vector

isoticks(ax, col)

Draws isometric projection of tick marks. :param ax: Axis object :param col: Color of ticks :return: None

make_isomatrices()

Make projection matrix, self.pc, for calculating isometric projection :return: None

unidec.modules.plotting.plot_waterfall module

class unidec.modules.plotting.plot_waterfall.Waterfall3DPlot(*args, **kwargs)

Bases: PlottingWindowBase

Plotting class for 3D Waterfall plots.

get_angle()
onmove(e=None)
set_angle(elevation, azimuth)
waterfall(xgrid, ygrid, zarray, colors=None, xlabel='Mass', ylabel='')
class unidec.modules.plotting.plot_waterfall.WaterfallFrame(parent)

Bases: Frame

change(e=None)
change_type(e=None)
draw()
make_plot(data=None)
onmove(e=None)
unidec.modules.plotting.plot_waterfall.cc(arg)

Module contents