def scatterplot(self,
xdata,
ydata,
label=None,
size=10,
color=None,
edgecolor=None,
selectcolor=None,
selectedge=None,
xlabel=None,
ylabel=None,
y2label=None,
xmin=None,
xmax=None,
ymin=None,
ymax=None,
title=None,
grid=None,
callback=None,
**kw):
if xlabel is not None:
self.set_xlabel(xlabel)
if ylabel is not None:
self.set_ylabel(ylabel)
if y2label is not None:
self.set_y2label(y2label)
if title is not None:
self.set_title(title)
if grid is not None:
self.conf.show_grid = grid
if callback is not None:
self.lasso_callback = callback
self.conf.plot_type = 'scatter'
self.cursor_mode = 'lasso'
if color is not None:
self.conf.scatter_normalcolor = color
if edgecolor is not None:
self.conf.scatter_normaledge = edgecolor
if selectcolor is not None:
self.conf.scatter_selectcolor = selectcolor
if selectedge is not None:
self.conf.scatter_selectedge = selectedge
axes = self.axes
self.conf.user_limits[axes] = (xmin, xmax, ymin, ymax)
self.conf.axes_traces = {axes: [0]}
self.conf.set_trace_label('scatterplot')
self.conf.set_trace_datarange(
(min(xdata), max(xdata), min(ydata), max(ydata)))
fcols = [to_rgba(self.conf.scatter_normalcolor) for x in xdata]
ecols = [self.conf.scatter_normaledge] * len(xdata)
self.conf.scatter_data = [(x, y) for x, y in zip(xdata, ydata)]
self.conf.scatter_size = size
self.conf.scatter_coll = CircleCollection(
sizes=(size, ),
facecolors=fcols,
edgecolors=ecols,
offsets=self.conf.scatter_data,
transOffset=self.axes.transData)
self.axes.add_collection(self.conf.scatter_coll)
if self.conf.show_grid:
for i in axes.get_xgridlines() + axes.get_ygridlines():
i.set_color(self.conf.gridcolor)
i.set_zorder(-30)
axes.grid(True)
else:
axes.grid(False)
self.set_viewlimits()
self.draw()
def freq_Scatter(parser, thrPrt=0.3, thrPep=0.5,
analysis_name = "",
Xlab = "", Ylab = "" ):
"""
plots an advanced scatter-plot for peptides and protein frequencies.
:param parser: the parser that store the seq
:param analysis_name: the analysis name
:param thrPrt: the protein frequency threshold
:param thrPep: the peptide frequency threshold
:param Xlab: the label for X axe
:param Ylab: the label for Y axe
:return: the figure of the analysis plot - after it can be plotted on the screen
or saved in a picture file
:raises NoData: If there are not proteins or peptides frequencies values
.. plot:: pyplots/scatter.py
:include-source:
"""
# calculating the plotting seq
x, y, z = parser.frequencyMatrix()
if x and y and z:
# definitions for the axes
left, width = 0.1, 0.65
bottom, height = 0.1, 0.65
bottom_b = left_b = left+width+0.01
rect_scatter = [left, bottom, width, height]
rect_box_x = [left, bottom_b, width, 0.2]
rect_box_y = [left_b, bottom, 0.2, height]
rect_leg = [left_b, bottom_b, 0.2, 0.2]
# start with a rectangular Figure
fig = plt.figure(scatter_plot_fig, figsize=(8,8))
axScatter = plt.axes(rect_scatter)
axBoxx = plt.axes(rect_box_x, xticks=[], yticks=[])
axBoxy = plt.axes(rect_box_y, xticks=[], yticks=[])
axLeg = plt.axes(rect_leg, xticks=[], yticks=[])
# no labels
import matplotlib.ticker
nullfmt = matplotlib.ticker.NullFormatter()
axBoxx.xaxis.set_major_formatter(nullfmt)
axBoxx.yaxis.set_major_formatter(nullfmt)
axBoxy.xaxis.set_major_formatter(nullfmt)
axBoxy.yaxis.set_major_formatter(nullfmt)
axLeg.xaxis.set_major_formatter(nullfmt)
axLeg.yaxis.set_major_formatter(nullfmt)
# scatter plot
axScatter.scatter(x, y, s=z, alpha=0.75)
axScatter.set_xlabel(Xlab)
axScatter.set_ylabel(Ylab)
axScatter.axhline(linewidth=2, color='r',linestyle='-.', y=thrPep)
axScatter.axvline(linewidth=2, color='r',linestyle='-.', x=thrPrt)
axScatter.set_xlim( (-0.1, 1.1) )
axScatter.set_ylim( (-0.1, 1.1) )
# x boxplot
axBoxx.boxplot(x,vert = 0)
axBoxx.set_xlim( axScatter.get_xlim() )
# title upside axBox
axBoxx.set_title(analysis_name, x=0.6)
# y box plot
axBoxy.boxplot(y)
axBoxy.set_ylim( axScatter.get_ylim() )
# Legend
c_c = CircleCollection(sizes=(1, 10, 100),
offsets=[(0.1, 0.5), (0.5, 0.5), (0.9, 0.5)],
transOffset=axLeg.transData,
alpha=0.75)
axLeg.add_collection(c_c)
plt.text(0.1, 0.3, "1", ha="center", size=8)
plt.text(0.5, 0.3, "10", ha="center", size=8)
plt.text(0.9, 0.3, "100", ha="center", size=8)
fig.canvas.draw()
return fig
else:
raise NoData, "There aren't about frequencies!!!"
