def plotNumLegend(self, colVecL, breakL, nb_breaks, filename=None, legendDir=None, type='png', int_labels=False):
if filename is None:
filename = 'legend_%i_%i_%i' % (len(colVecL), min(breakL), max(breakL))
if legendDir is None:
legendDir = self.legendDir
full_filename = os.path.join(legendDir, filename)
max_break = max(breakL)
min_break = min(breakL)
tickBreakL = [float(x) / (nb_breaks - 1) * (max_break - min_break) - min_break for x in range(nb_breaks)]
if int_labels:
labels = ['%i' % int(x) for x in tickBreakL]
else:
labels = ['%.3f' % x for x in tickBreakL]
rdev = plot_utilities.RDevice(name = full_filename, title='', plotType=type,
width=640, height=120)
r("par(mar=c(3,1,0,1), las=2)")
#legendA = rpy.reshape(breakL, (len(breakL), 1))
legendA = r.matrix(breakL, byrow=False, ncol=1)
r.image(legendA, 1, legendA, col=colVecL, axes=False, ann=False)
r.box()
r.axis(1, at=tickBreakL, labels=labels, tick=True, line=0, cex=0.8, cex_axis=0.8)
rdev.close()
return
def plotArray(self, hitDataParam, filename, plotDir=None, labeledPosD=None,
title='', type='png',
label_colors = True, colVecL=None, legend_plot = False, legend_filename=None,
control_color='black', numeric_as_int = False,
grid=True, max_val=0.3, min_val=0.0, cut_data = True):
if plotDir is None:
plotDir = self.plotDir
full_filename = os.path.join(plotDir, filename)
#hitData = copy.deepcopy(hitDataParam)
hitData = hitDataParam
#nrow = len(hitData)
#ncol = len(hitData[0])
nrow = self.nb_row
ncol = self.nb_col
xL = range(1, self.nb_col + 1)
yL = range(1, self.nb_row + 1)
rdev = plot_utilities.RDevice(name = full_filename, title=title, plotType=type,
width=640, height=250)
if label_colors:
# in this case, the data is considered to consist of labels
labelL = []
for i in range(nrow):
for j in range(ncol):
if hitData[i][j] not in labelL:
labelL.append(hitData[i][j])
if colVecL is None:
colVecL = r.rainbow(len(labelL))
colBreaksL = range(len(colVecL) + 1)
if legend_plot:
self.plotLabelLegend(colVecL, plotType=type, filename=legend_filename)
else:
# in this case, the data is numeric.
if cut_data:
max_rel_cell_count = max_val
min_rel_cell_count = 0.0
for i in range(nrow):
for j in range(ncol):
hitData[i][j] = max(min_rel_cell_count, min(max_rel_cell_count, hitData[i][j]))
else:
max_rel_cell_count = max([max(x) for x in hitData.tolist() ])
min_rel_cell_count = min([min(x) for x in hitData.tolist() ])
if numeric_as_int:
nb_colors = max_rel_cell_count
else:
nb_colors = 500
if colVecL is None:
pattern = [(0,0,0),(0.7,0,0),(1,1,0),(1,1,1)]
colVecL = colors.make_colors(pattern, nb_colors)
colBreaksL = [1.0/ (len(colVecL) - 1) * x * (max_rel_cell_count - min_rel_cell_count) + min_rel_cell_count for x in range(len(colVecL) + 1)]
if legend_plot:
self.plotNumLegend(colVecL, colBreaksL, 16, filename=legend_filename, type=type, int_labels=numeric_as_int, legendDir = plotDir)
axisSize = .8
r("par(mar=c(1.6,1.6,0.1,0.1))")
r.image(xL, yL, r.t(hitData), axes = False, ann=False, cex=1, col=colVecL, breaks=colBreaksL)
r.box()
if not labeledPosD is None:
for label in labeledPosD.keys():
posL = labeledPosD[label]
if len(posL) > 0:
xlL = [(int(x)-1) % self.nb_col + 1 for x in posL]
ylL = [(int(x)-1) / self.nb_col + 1 for x in posL]
r.points(xlL, ylL, pch=label, col=control_color, cex=axisSize)
print
print xlL
print ylL
print
# grid
if grid:
for i in range(self.nb_col):
r.abline(h=i+.5, lty=3, lwd=1, col='grey')
for i in range(self.nb_row):
r.abline(v=i+.5, lty=3, lwd=1, col='grey')
r.axis(1, at=xL, labels=[str(x) for x in xL], tick=False, line=-1.0, cex_axis=axisSize)
r.axis(2, at=yL, labels=[str(y) for y in yL], tick=False, line=-1.0, cex_axis=axisSize)
rdev.close()
return
