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Coding style

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Alexander Minges 2015-07-08 01:03:25 +02:00
parent ddb879e80d
commit 1ef02beebb
1 changed files with 98 additions and 65 deletions
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pydsf.py
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@ -38,15 +38,14 @@ class Well:
Represents a well in a microtiter plate. Represents a well in a microtiter plate.
Owned by an object of type 'Plate'. Owned by an object of type 'Plate'.
""" """
def __init__(self, owner, name=None): def __init__(self, owner, name=None):
self.owner = owner self.owner = owner
self.name = name self.name = name
self.raw = np.zeros(self.owner.reads, dtype=np.float) self.raw = np.zeros(self.owner.reads, dtype=np.float)
self.filtered = np.zeros(self.owner.reads, dtype=np.float) self.filtered = np.zeros(self.owner.reads, dtype=np.float)
self.derivatives = np.zeros((4, self.owner.reads)) self.derivatives = np.zeros((4, self.owner.reads))
self.splines = {"raw": None, self.splines = {"raw": None, "filtered": None, "derivative1": None}
"filtered": None,
"derivative1": None}
self.tm = np.NaN self.tm = np.NaN
self.tm_sd = np.NaN self.tm_sd = np.NaN
self.baseline_correction = owner.baseline_correction self.baseline_correction = owner.baseline_correction
@ -115,8 +114,7 @@ class Well:
if (self.owner.tm_cutoff_low != self.owner.t1 or if (self.owner.tm_cutoff_low != self.owner.t1 or
self.owner.tm_cutoff_high != self.owner.t1): self.owner.tm_cutoff_high != self.owner.t1):
x = np.arange(self.owner.tm_cutoff_low, x = np.arange(self.owner.tm_cutoff_low,
self.owner.tm_cutoff_high + 1, self.owner.tm_cutoff_high + 1, self.owner.dt,
self.owner.dt,
dtype=np.dtype(np.float)) dtype=np.dtype(np.float))
# Otherwise use the whole temperature range of the data # Otherwise use the whole temperature range of the data
else: else:
@ -158,7 +156,8 @@ class Well:
try: try:
if (tm and tm >= self.owner.tm_cutoff_low and if (tm and tm >= self.owner.tm_cutoff_low and
tm <= self.owner.tm_cutoff_high): tm <= self.owner.tm_cutoff_high):
tm = round(peakutils.interpolate(x, y, width=3, tm = round(peakutils.interpolate(x, y,
width=3,
ind=[max_i])[0], 2) ind=[max_i])[0], 2)
self.owner.denatured_wells.remove(self) self.owner.denatured_wells.remove(self)
# If everything is fine, remove the denatured flag # If everything is fine, remove the denatured flag
@ -240,9 +239,19 @@ class Well:
class Experiment: class Experiment:
def __init__(self, exp_type, gui=None, files=None, replicates=None, t1=25, def __init__(self, exp_type,
t2=95, dt=1, cols=12, rows=8, cutoff_low=None, gui=None,
cutoff_high=None, signal_threshold=None, color_range=None, files=None,
replicates=None,
t1=25,
t2=95,
dt=1,
cols=12,
rows=8,
cutoff_low=None,
cutoff_high=None,
signal_threshold=None,
color_range=None,
baseline_correction=False): baseline_correction=False):
self.replicates = replicates self.replicates = replicates
self.cols = cols self.cols = cols
@ -284,9 +293,15 @@ class Experiment:
# populate self.plates with data in provided files list # populate self.plates with data in provided files list
i = 1 i = 1
for file in files: for file in files:
plate = Plate(plate_type=self.type, owner=self, filename=file, plate = Plate(plate_type=self.type,
t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols, owner=self,
rows=self.rows, cutoff_low=self.tm_cutoff_low, filename=file,
t1=self.t1,
t2=self.t2,
dt=self.dt,
cols=self.cols,
rows=self.rows,
cutoff_low=self.tm_cutoff_low,
cutoff_high=self.tm_cutoff_high, cutoff_high=self.tm_cutoff_high,
signal_threshold=self.signal_threshold, signal_threshold=self.signal_threshold,
color_range=self.color_range) color_range=self.color_range)
@ -296,9 +311,14 @@ class Experiment:
# if more than one file is provied, assume that those are replicates # if more than one file is provied, assume that those are replicates
# and add a special plate representing the average results # and add a special plate representing the average results
if len(files) > 1: if len(files) > 1:
self.avg_plate = Plate(plate_type=self.type, owner=self, self.avg_plate = Plate(plate_type=self.type,
filename=None, t1=self.t1, t2=self.t2, owner=self,
dt=self.dt, cols=self.cols, rows=self.rows, filename=None,
t1=self.t1,
t2=self.t2,
dt=self.dt,
cols=self.cols,
rows=self.rows,
cutoff_low=self.tm_cutoff_low, cutoff_low=self.tm_cutoff_low,
cutoff_high=self.tm_cutoff_high, cutoff_high=self.tm_cutoff_high,
signal_threshold=self.signal_threshold, signal_threshold=self.signal_threshold,
@ -337,9 +357,18 @@ class Experiment:
class Plate: class Plate:
def __init__(self, plate_type, owner, plate_id=None, filename=None, def __init__(self, plate_type, owner,
replicates=None, t1=None, t2=None, dt=None, cols=12, rows=8, plate_id=None,
cutoff_low=None, cutoff_high=None, signal_threshold=None, filename=None,
replicates=None,
t1=None,
t2=None,
dt=None,
cols=12,
rows=8,
cutoff_low=None,
cutoff_high=None,
signal_threshold=None,
color_range=None): color_range=None):
self.cols = cols self.cols = cols
self.rows = rows self.rows = rows
@ -453,13 +482,11 @@ class Plate:
def write_avg_tm_table(self, filename): def write_avg_tm_table(self, filename):
with open(filename, 'w') as f: with open(filename, 'w') as f:
f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"', f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"', '"Tm [°C]"',
'"Tm [°C]"',
'"SD"')) '"SD"'))
for well in self.wells: for well in self.wells:
if np.isnan(well.tm) or well in self.denatured_wells: if np.isnan(well.tm) or well in self.denatured_wells:
f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, 'NaN',
'NaN',
'NaN')) 'NaN'))
else: else:
f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name,
@ -531,7 +558,6 @@ def update_progress_bar(bar, value):
class PlotResults(): class PlotResults():
def plot_tm_heatmap_single(self, plate, widget): def plot_tm_heatmap_single(self, plate, widget):
""" """
Plot Tm heatmap (Fig. 1) Plot Tm heatmap (Fig. 1)
@ -579,16 +605,24 @@ class PlotResults():
# n rows # n rows
if plate.color_range: if plate.color_range:
# plot wells and color using the colormap # plot wells and color using the colormap
cax = ax1.scatter(x_values, y_values, s=305, c=c_values, cax = ax1.scatter(x_values, y_values,
marker='s', vmin=plate.color_range[0], s=305,
c=c_values,
marker='s',
vmin=plate.color_range[0],
vmax=plate.color_range[1]) vmax=plate.color_range[1])
else: else:
# plot wells and color using the colormap # plot wells and color using the colormap
cax = ax1.scatter(x_values, y_values, s=305, c=c_values, cax = ax1.scatter(x_values, y_values,
s=305,
c=c_values,
marker='s') marker='s')
ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x', ax1.scatter(dx_values, dy_values,
linewidths=(1.5,)) s=80,
c='white',
marker='x',
linewidths=(1.5, ))
ax1.invert_yaxis() # invert y axis to math plate layout ax1.invert_yaxis() # invert y axis to math plate layout
cbar = fig1.colorbar(cax) # show colorbar cbar = fig1.colorbar(cax) # show colorbar
ax1.set_xlabel('Columns') # set axis and colorbar label ax1.set_xlabel('Columns') # set axis and colorbar label
@ -609,37 +643,34 @@ class PlotResults():
""" """
canvas = widget.canvas canvas = widget.canvas
canvas.clear() canvas.clear()
fig2 = canvas.fig # new figure fig = canvas.fig # new figure
# set title # set title
fig2.suptitle( fig.suptitle(
'Individual Derivatives (plate #{})'.format(str(plate.id))) 'Individual Derivatives (plate #{})'.format(str(plate.id)))
for plot_num in range(1, plate.wellnum + 1): # iterate over all wells grid = mpl_toolkits.axes_grid1.Grid(
well = plate.wells[plot_num - 1] fig, 111,
# get single well based on current plot number nrows_ncols=(plate.rows, plate.cols),
ax = fig2.add_subplot(plate.rows, plate.cols, plot_num) axes_pad=(0.15, 0.25),
# add new subplot add_all=True,
ax.autoscale(tight=True) # scale to data share_all=True)
ax.set_title(well.name, size='xx-small')
# set title of current subplot to well identifier
if well in plate.denatured_wells:
ax.patch.set_facecolor('#FFD6D6')
# add axis label to the subplot in the bottom left corner of the
# figure
if plot_num == plate.wellnum - plate.cols + 1:
ax.set_xlabel(u'T [°C]', size='xx-small')
ax.set_ylabel('dI/dT', size='xx-small')
for i in range(plate.wellnum):
well = plate.wells[i]
# set values for the x axis to the given temperature range # set values for the x axis to the given temperature range
x = plate.temprange x = plate.temprange
# grab y values from the raw data of the well
if well.baseline_correction: if well.baseline_correction:
print(well.baseline) print(well.baseline)
y = well.derivatives[1] - well.baseline y = well.derivatives[1] - well.baseline
else: else:
# grab y values from the first derivative of the well # grab y values from the first derivative of the well
y = well.derivatives[1] y = well.derivatives[1]
ax = grid[i]
# set title of current subplot to well identifier
ax.set_title(well.name, size=6)
if well in plate.denatured_wells:
ax.patch.set_facecolor('#FFD6D6')
# only show three tickmarks on both axes # only show three tickmarks on both axes
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
ax.yaxis.set_major_locator(ticker.MaxNLocator(4)) ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
@ -650,15 +681,20 @@ class PlotResults():
tm = np.NaN # else set Tm to np.NaN tm = np.NaN # else set Tm to np.NaN
if tm: if tm:
ax.axvline(x=tm) # plot vertical line at the Tm ax.axvline(x=tm) # plot vertical line at the Tm
ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8', ax.axvspan(plate.t1, plate.tm_cutoff_low,
facecolor='0.8',
alpha=0.5) # shade lower cutoff area alpha=0.5) # shade lower cutoff area
ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', ax.axvspan(plate.tm_cutoff_high, plate.t2,
facecolor='0.8',
alpha=0.5) # shade higher cutoff area alpha=0.5) # shade higher cutoff area
# set fontsize for all tick labels to xx-small # set fontsize for all tick labels to xx-small
for label in ax.get_xticklabels() + ax.get_yticklabels(): for label in ax.get_xticklabels() + ax.get_yticklabels():
label.set_fontsize('xx-small') label.set_fontsize(6)
ax.plot(x, y)
ax.plot(x, y) # plot data to the current subplot # if plot_num == plate.wellnum - plate.cols + 1:
# ax.set_xlabel(u'T [°C]', size='xx-small')
# ax.set_ylabel(u'dI/dT', size='xx-small')
fig.tight_layout()
canvas.draw() canvas.draw()
def plot_raw(self, plate, widget): def plot_raw(self, plate, widget):
@ -668,20 +704,15 @@ class PlotResults():
canvas = widget.canvas canvas = widget.canvas
canvas.clear() canvas.clear()
im = np.arange(100)
im.shape = 10, 10
fig = canvas.fig fig = canvas.fig
fig.suptitle('Raw Data (plate #{})'.format(str(plate.id))) fig.suptitle('Raw Data (plate #{})'.format(str(plate.id)))
grid = mpl_toolkits.axes_grid1.Grid(fig, 111, grid = mpl_toolkits.axes_grid1.Grid(
nrows_ncols=(plate.rows, fig, 111,
plate.cols), nrows_ncols=(plate.rows, plate.cols),
axes_pad=(0.1, 0.25), axes_pad=(0.15, 0.25),
add_all=True, add_all=True,
share_x=True, share_all=True)
share_y=True,
share_all=True)
for i in range(plate.wellnum): for i in range(plate.wellnum):
well = plate.wells[i] well = plate.wells[i]
# set values for the x axis to the given temperature range # set values for the x axis to the given temperature range
@ -696,9 +727,11 @@ class PlotResults():
# only show three tickmarks on both axes # only show three tickmarks on both axes
ax.xaxis.set_major_locator(ticker.MaxNLocator(4)) ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
ax.yaxis.set_major_locator(ticker.MaxNLocator(4)) ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8', ax.axvspan(plate.t1, plate.tm_cutoff_low,
facecolor='0.8',
alpha=0.5) # shade lower cutoff area alpha=0.5) # shade lower cutoff area
ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8', ax.axvspan(plate.tm_cutoff_high, plate.t2,
facecolor='0.8',
alpha=0.5) # shade higher cutoff area alpha=0.5) # shade higher cutoff area
# set fontsize for all tick labels to xx-small # set fontsize for all tick labels to xx-small
for label in ax.get_xticklabels() + ax.get_yticklabels(): for label in ax.get_xticklabels() + ax.get_yticklabels():