def generateDensityPlots(self, labtekId, resD):
labeledPosD = {'s': self.lc.negCtrPosL,
'-': self.lc.emptyL}
idL = filter(lambda x: x.split('--')[0] == labtekId, resD.keys())
idL.sort()
pattern = [(0,0,0), (0,0,0.5), (0,1,1), (1,1,1)]
colVecL = colors.make_colors(pattern, 500)
settingL = [
{'min': 15, 'max': 800, 'colVecL': None},
{'min': 15, 'max': 800, 'colVecL': None},
{'min': 0.0, 'max': 4.0, 'colVecL': colVecL}
]
# init cell count
for pheno, setting in zip(['initCellCount', 'endCellCount', 'proliferation'], settingL):
plotDir = os.path.join(self.html_dir, 'plots', labtekId)
if not os.path.isdir(plotDir):
os.makedirs(plotDir)
filename = '%s--%s' % (pheno, labtekId)
data = self.ap.prepareData(resD, self.ap.getPhenoVal(pheno), idL)
self.ap.plotArray(data, filename, plotDir=plotDir, colVecL=setting['colVecL'],
min_val=setting['min'], max_val=setting['max'],
label_colors = False, labeledPosD=labeledPosD,
legend_plot = True, legend_filename='legend_%s' % filename)
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
def generateDensityPlots(self, labtekId, resD):
labeledPosD = {'s': ['015', '026', '063', '074', '304', '315', '352'],
'b' : ['363'],
'e' : ['290', '301', '338', '349'],
'i' : ['004', '049', '052'],
'm' : ['001']
}
idL = filter(lambda x: x.split('--')[0] == labtekId, resD.keys())
idL.sort()
#pattern = [(0,0,0), (0,0,1), (0,0.5,1), (1,1,1)]
# pattern = [(0.00, 0.10, 0.30)
# (0.00, 0.22, 0.61),
# (0.1, 0.31, 0.74),
# (0.3, 0.48, 0.84),
# (0.6, 0.64, 0.91),
# (0.94, 0.95, 1.00)]
pattern = get_color_brewer_pattern("YlGnBu")
col2 = colors.make_colors(pattern, 500)
# pattern = [(0, 0, 0),
# (0.0, 0.26, 0.1),
# (0.0, 0.43, 0.17),
# (0.1, 0.54, 0.27),
# (0.2, 0.67, 0.36),
# (0.3, 0.77, 0.46),
# (0.4, 0.85, 0.60),
# (0.6, 0.91, 0.75),
# (0.8, 0.96, 0.88),
# (0.97, 0.98, 1.0)]
# pattern = [(0,0,0), (0,0.5,0), (0.3,1,0), (1,1,1)]
pattern = get_color_brewer_pattern("YlGn")
col1 = colors.make_colors(pattern, 500)
#paletteName = 'RdPu'
#colRampFunc = r.colorRampPalette(brewer.pal(9, paletteName))
#colVec = colRampFunc(384)
settingL = [
{'min': 0.0, 'max': 80.0, 'colVecL': col1},
{'min': 0.0, 'max': 100.0, 'colVecL': col2},
{'min': 0, 'max': 800, 'colVecL': None},
{'min': 0, 'max': 384, 'colVecL': None},
{'min': 0.0, 'max': 100.0, 'colVecL': col2},
]
# init cell count
for pheno, setting in zip(['ratio', 'fractionIndex', 'number', 'pos', 'fractionIndexPlateThresh'], settingL):
plotDir = os.path.join(self.html_dir, 'plots', labtekId)
if not os.path.isdir(plotDir):
os.makedirs(plotDir)
filename = '%s--%s' % (pheno, labtekId)
data = self.ap.prepareData(resD, self.ap.getPhenoVal(pheno), idL)
self.ap.plotArray(data, filename, plotDir=plotDir, colVecL=setting['colVecL'],
min_val=setting['min'], max_val=setting['max'],
label_colors = False, labeledPosD=labeledPosD,
legend_plot = True, legend_filename='legend_%s' % filename)
filename = 'Rotate--%s--%s' % (pheno, labtekId)
data = self.ap.prepareData(resD, self.ap.getPhenoVal(pheno), idL, flip_axis=True)
self.ap.plotArray(data, filename, plotDir=plotDir, colVecL=setting['colVecL'],
min_val=setting['min'], max_val=setting['max'],
label_colors = False, labeledPosD={},
legend_plot = False, flip_axis=True, axis=False)
return