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Coding style
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1 changed files with 98 additions and 65 deletions
163
pydsf.py
163
pydsf.py
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@ -38,15 +38,14 @@ class Well:
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Represents a well in a microtiter plate.
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Owned by an object of type 'Plate'.
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"""
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def __init__(self, owner, name=None):
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self.owner = owner
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self.name = name
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self.raw = np.zeros(self.owner.reads, dtype=np.float)
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self.filtered = np.zeros(self.owner.reads, dtype=np.float)
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self.derivatives = np.zeros((4, self.owner.reads))
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self.splines = {"raw": None,
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"filtered": None,
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"derivative1": None}
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self.splines = {"raw": None, "filtered": None, "derivative1": None}
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self.tm = np.NaN
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self.tm_sd = np.NaN
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self.baseline_correction = owner.baseline_correction
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@ -115,8 +114,7 @@ class Well:
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if (self.owner.tm_cutoff_low != self.owner.t1 or
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self.owner.tm_cutoff_high != self.owner.t1):
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x = np.arange(self.owner.tm_cutoff_low,
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self.owner.tm_cutoff_high + 1,
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self.owner.dt,
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self.owner.tm_cutoff_high + 1, self.owner.dt,
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dtype=np.dtype(np.float))
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# Otherwise use the whole temperature range of the data
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else:
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@ -158,7 +156,8 @@ class Well:
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try:
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if (tm and tm >= self.owner.tm_cutoff_low and
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tm <= self.owner.tm_cutoff_high):
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tm = round(peakutils.interpolate(x, y, width=3,
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tm = round(peakutils.interpolate(x, y,
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width=3,
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ind=[max_i])[0], 2)
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self.owner.denatured_wells.remove(self)
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# If everything is fine, remove the denatured flag
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@ -240,9 +239,19 @@ class Well:
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class Experiment:
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def __init__(self, exp_type, gui=None, files=None, replicates=None, t1=25,
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t2=95, dt=1, cols=12, rows=8, cutoff_low=None,
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cutoff_high=None, signal_threshold=None, color_range=None,
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def __init__(self, exp_type,
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gui=None,
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files=None,
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replicates=None,
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t1=25,
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t2=95,
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dt=1,
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cols=12,
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rows=8,
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cutoff_low=None,
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cutoff_high=None,
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signal_threshold=None,
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color_range=None,
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baseline_correction=False):
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self.replicates = replicates
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self.cols = cols
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@ -284,9 +293,15 @@ class Experiment:
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# populate self.plates with data in provided files list
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i = 1
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for file in files:
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plate = Plate(plate_type=self.type, owner=self, filename=file,
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t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols,
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rows=self.rows, cutoff_low=self.tm_cutoff_low,
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plate = Plate(plate_type=self.type,
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owner=self,
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filename=file,
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t1=self.t1,
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t2=self.t2,
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dt=self.dt,
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cols=self.cols,
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rows=self.rows,
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cutoff_low=self.tm_cutoff_low,
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cutoff_high=self.tm_cutoff_high,
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signal_threshold=self.signal_threshold,
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color_range=self.color_range)
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@ -296,9 +311,14 @@ class Experiment:
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# if more than one file is provied, assume that those are replicates
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# and add a special plate representing the average results
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if len(files) > 1:
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self.avg_plate = Plate(plate_type=self.type, owner=self,
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filename=None, t1=self.t1, t2=self.t2,
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dt=self.dt, cols=self.cols, rows=self.rows,
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self.avg_plate = Plate(plate_type=self.type,
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owner=self,
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filename=None,
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t1=self.t1,
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t2=self.t2,
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dt=self.dt,
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cols=self.cols,
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rows=self.rows,
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cutoff_low=self.tm_cutoff_low,
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cutoff_high=self.tm_cutoff_high,
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signal_threshold=self.signal_threshold,
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@ -337,9 +357,18 @@ class Experiment:
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class Plate:
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def __init__(self, plate_type, owner, plate_id=None, filename=None,
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replicates=None, t1=None, t2=None, dt=None, cols=12, rows=8,
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cutoff_low=None, cutoff_high=None, signal_threshold=None,
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def __init__(self, plate_type, owner,
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plate_id=None,
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filename=None,
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replicates=None,
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t1=None,
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t2=None,
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dt=None,
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cols=12,
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rows=8,
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cutoff_low=None,
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cutoff_high=None,
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signal_threshold=None,
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color_range=None):
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self.cols = cols
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self.rows = rows
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@ -453,13 +482,11 @@ class Plate:
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def write_avg_tm_table(self, filename):
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with open(filename, 'w') as f:
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f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"',
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'"Tm [°C]"',
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f.write('#{:<4s}{:>13s}{:>13s}\n'.format('"ID"', '"Tm [°C]"',
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'"SD"'))
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for well in self.wells:
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if np.isnan(well.tm) or well in self.denatured_wells:
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f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name,
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'NaN',
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f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name, 'NaN',
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'NaN'))
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else:
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f.write('{:<5s}{:>12s}{:>12s}\n'.format(well.name,
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@ -531,7 +558,6 @@ def update_progress_bar(bar, value):
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class PlotResults():
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def plot_tm_heatmap_single(self, plate, widget):
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"""
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Plot Tm heatmap (Fig. 1)
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@ -579,16 +605,24 @@ class PlotResults():
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# n rows
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if plate.color_range:
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# plot wells and color using the colormap
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cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
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marker='s', vmin=plate.color_range[0],
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cax = ax1.scatter(x_values, y_values,
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s=305,
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c=c_values,
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marker='s',
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vmin=plate.color_range[0],
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vmax=plate.color_range[1])
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else:
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# plot wells and color using the colormap
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cax = ax1.scatter(x_values, y_values, s=305, c=c_values,
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cax = ax1.scatter(x_values, y_values,
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s=305,
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c=c_values,
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marker='s')
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ax1.scatter(dx_values, dy_values, s=80, c='white', marker='x',
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linewidths=(1.5,))
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ax1.scatter(dx_values, dy_values,
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s=80,
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c='white',
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marker='x',
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linewidths=(1.5, ))
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ax1.invert_yaxis() # invert y axis to math plate layout
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cbar = fig1.colorbar(cax) # show colorbar
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ax1.set_xlabel('Columns') # set axis and colorbar label
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@ -609,37 +643,34 @@ class PlotResults():
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"""
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canvas = widget.canvas
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canvas.clear()
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fig2 = canvas.fig # new figure
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fig = canvas.fig # new figure
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# set title
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fig2.suptitle(
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fig.suptitle(
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'Individual Derivatives (plate #{})'.format(str(plate.id)))
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for plot_num in range(1, plate.wellnum + 1): # iterate over all wells
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well = plate.wells[plot_num - 1]
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# get single well based on current plot number
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ax = fig2.add_subplot(plate.rows, plate.cols, plot_num)
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# add new subplot
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ax.autoscale(tight=True) # scale to data
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ax.set_title(well.name, size='xx-small')
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# set title of current subplot to well identifier
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if well in plate.denatured_wells:
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ax.patch.set_facecolor('#FFD6D6')
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# add axis label to the subplot in the bottom left corner of the
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# figure
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if plot_num == plate.wellnum - plate.cols + 1:
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ax.set_xlabel(u'T [°C]', size='xx-small')
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ax.set_ylabel('dI/dT', size='xx-small')
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grid = mpl_toolkits.axes_grid1.Grid(
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fig, 111,
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nrows_ncols=(plate.rows, plate.cols),
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axes_pad=(0.15, 0.25),
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add_all=True,
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share_all=True)
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for i in range(plate.wellnum):
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well = plate.wells[i]
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# set values for the x axis to the given temperature range
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x = plate.temprange
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# grab y values from the raw data of the well
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if well.baseline_correction:
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print(well.baseline)
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y = well.derivatives[1] - well.baseline
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else:
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# grab y values from the first derivative of the well
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y = well.derivatives[1]
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ax = grid[i]
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# set title of current subplot to well identifier
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ax.set_title(well.name, size=6)
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if well in plate.denatured_wells:
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ax.patch.set_facecolor('#FFD6D6')
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# only show three tickmarks on both axes
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ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
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ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
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@ -650,15 +681,20 @@ class PlotResults():
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tm = np.NaN # else set Tm to np.NaN
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if tm:
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ax.axvline(x=tm) # plot vertical line at the Tm
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ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
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ax.axvspan(plate.t1, plate.tm_cutoff_low,
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facecolor='0.8',
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alpha=0.5) # shade lower cutoff area
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ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
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ax.axvspan(plate.tm_cutoff_high, plate.t2,
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facecolor='0.8',
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alpha=0.5) # shade higher cutoff area
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# set fontsize for all tick labels to xx-small
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for label in ax.get_xticklabels() + ax.get_yticklabels():
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label.set_fontsize('xx-small')
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ax.plot(x, y) # plot data to the current subplot
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label.set_fontsize(6)
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ax.plot(x, y)
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# if plot_num == plate.wellnum - plate.cols + 1:
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# ax.set_xlabel(u'T [°C]', size='xx-small')
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# ax.set_ylabel(u'dI/dT', size='xx-small')
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fig.tight_layout()
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canvas.draw()
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def plot_raw(self, plate, widget):
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@ -668,20 +704,15 @@ class PlotResults():
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canvas = widget.canvas
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canvas.clear()
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im = np.arange(100)
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im.shape = 10, 10
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fig = canvas.fig
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fig.suptitle('Raw Data (plate #{})'.format(str(plate.id)))
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grid = mpl_toolkits.axes_grid1.Grid(fig, 111,
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nrows_ncols=(plate.rows,
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plate.cols),
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axes_pad=(0.1, 0.25),
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add_all=True,
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share_x=True,
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share_y=True,
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share_all=True)
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grid = mpl_toolkits.axes_grid1.Grid(
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fig, 111,
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nrows_ncols=(plate.rows, plate.cols),
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axes_pad=(0.15, 0.25),
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add_all=True,
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share_all=True)
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for i in range(plate.wellnum):
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well = plate.wells[i]
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# set values for the x axis to the given temperature range
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@ -696,9 +727,11 @@ class PlotResults():
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# only show three tickmarks on both axes
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ax.xaxis.set_major_locator(ticker.MaxNLocator(4))
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ax.yaxis.set_major_locator(ticker.MaxNLocator(4))
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ax.axvspan(plate.t1, plate.tm_cutoff_low, facecolor='0.8',
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ax.axvspan(plate.t1, plate.tm_cutoff_low,
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facecolor='0.8',
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alpha=0.5) # shade lower cutoff area
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ax.axvspan(plate.tm_cutoff_high, plate.t2, facecolor='0.8',
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ax.axvspan(plate.tm_cutoff_high, plate.t2,
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facecolor='0.8',
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alpha=0.5) # shade higher cutoff area
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# set fontsize for all tick labels to xx-small
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for label in ax.get_xticklabels() + ax.get_yticklabels():
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