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Merge pull request pydna-group#18 from bruno2git/master
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Addressed the issue of DNA bands not visible on Gel electrophoresis
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@BjornFJohansson
BjornFJohansson authored Jun 24, 2016
2 parents 2e0a84d + 5368e96 commit 406664a
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Showing 2 changed files with 34 additions and 16 deletions.
2 changes: 1 addition & 1 deletion pydna/dsdna.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1371,7 +1371,7 @@ class Dseqrecord(SeqRecord):
def __init__(self, record,
circular = None,
linear = None,
n = 10E-12, # mol (10 pmol)
n = 5E-14, # mol (0.05 pmol)
*args,
**kwargs):
self.n = n
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48 changes: 33 additions & 15 deletions pydna/gel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -778,27 +778,30 @@ def ferguson_to_mu0(field, Tvals, DNAvals, dataset, mu_func,

def gelplot_imshow(distances, bandwidths, intensities, lanes, names,
gel_len, wellx, welly, wellsep, res, cursor_ovr,
back_col, band_col, well_col, noise, Itol, title,
back_col, band_col, well_col, noise, Itol, detectlim, title,
FWTM, show=True):
nlanes = len(lanes)
gel_width = sum(wellx) + (nlanes+1)*wellsep # cm
res = res.to('px/cm')
pxl_x = int(round(gel_width * res))
pxl_y = int(round(gel_len * res))
centers = [(l+1)*wellsep + sum(wellx[:l]) + 0.5*wellx[l]
for l in xrange(nlanes)]
lane_centers = [(l+1)*wellsep + sum(wellx[:l]) + 0.5*wellx[l]
for l in xrange(nlanes)]
rgb_arr = np.zeros(shape=(pxl_y, pxl_x, 3), dtype=np.float32)
bandlengths = wellx
bands_pxlXYmid = []
# Paint the bands
for i in xrange(nlanes):
distXmid = centers[i]
pxlXmid = distXmid * res
distXmid = lane_centers[i]
pxlXmid = int(round(distXmid * res))
bandlength = bandlengths[i]
from_x = int(round((distXmid - bandlength/2.0) * res))
to_x = int(round((distXmid + bandlength/2.0) * res))
bands_pxlXYmid.append([])
for j in xrange(len(lanes[i])):
distYmid = distances[i][j]
pxlYmid = int(round(distYmid * res))
bands_pxlXYmid[i].append((pxlXmid, pxlYmid))
bandwidth = bandwidths[i][j] # w=FWHM or w=FWTM ???
if FWTM:
FWHM = Gauss_FWHM(bandwidth)
Expand Down Expand Up @@ -847,7 +850,7 @@ def gelplot_imshow(distances, bandwidths, intensities, lanes, names,
wellx = wellx.magnitude
welly = welly.magnitude
wellsep = wellsep.magnitude
centers = [c.magnitude for c in centers]
lane_centers = [c.magnitude for c in lane_centers]
bandlengths = bandlengths.magnitude
bandwidths = [[bw.magnitude for bw in bwlane] for bwlane in bandwidths]
fig = plt.figure()
Expand All @@ -862,19 +865,20 @@ def gelplot_imshow(distances, bandwidths, intensities, lanes, names,
ax1.spines['right'].set_color(str(back_col))
ax1.spines['bottom'].set_color(str(back_col))
ax1.xaxis.set_label_position('top')
plt.xticks(centers, names)
plt.xticks(lane_centers, names)
majorLocator = FixedLocator(range(int(gel_len+1)))
minorLocator = FixedLocator([j/10.0 for k in
range(0, int(gel_len+1)*10, 10)
for j in range(1+k, 10+k, 1)])
ax1.yaxis.set_major_locator(majorLocator)
ax1.yaxis.set_minor_locator(minorLocator)
ax1.tick_params(axis='x', which='both', top='off')
# Gel image
bands_plt = ax1.imshow(bands_arr, extent=[0, gel_width, gel_len, 0],
interpolation='none')
# Draw wells
for i in xrange(nlanes):
ctr = centers[i]
ctr = lane_centers[i]
wx = wellx[i]
wy = welly[i]
ax1.fill_between(x=[ctr-wx/2, ctr+wx/2], y1=[0, 0],
Expand All @@ -883,15 +887,19 @@ def gelplot_imshow(distances, bandwidths, intensities, lanes, names,
bands = []
for i in xrange(nlanes):
bandlength = bandlengths[i]
center = centers[i]
center = lane_centers[i]
x = center - bandlength/2.0
for j in xrange(len(lanes[i])):
dna_frag = lanes[i][j]
bandwidth = bandwidths[i][j]
dist = distances[i][j].magnitude
y = dist - bandwidth/2.0
band = plt.Rectangle((x, y), bandlength, bandwidth, fc='r',
alpha=0, label='{} bp'.format(len(dna_frag)))
pxlX, pxlY = bands_pxlXYmid[i][j]
band_midI = bands_arr[pxlY, pxlX][0]
alpha = 0 if abs(band_midI - back_col) >= detectlim else 0.4
band = plt.Rectangle((x, y), bandlength, bandwidth,
fc='none', ec='w', ls=':', alpha=alpha,
label='{} bp'.format(len(dna_frag)))
plt.gca().add_patch(band)
bands.append(band)
plt.ylim(gel_len, -max(welly))
Expand Down Expand Up @@ -1089,6 +1097,7 @@ def run(self,
band_col=1,
well_col=0.05,
noise=0.015,
detectlim=0.04,
interpol='linear', # 'cubic','nearest'
dset_name='vertical', # 'horizontal'
replNANs=True # replace NANs by 'nearest' interpolation
Expand Down Expand Up @@ -1167,6 +1176,13 @@ def run(self,
aesthetic.
Defaults to 0.015.
detectlim : float, optional
Minimal light intensity difference between the center of the band
and the background color (back_col) below which the band is
considered to be indistinguishable and a white doted outline is
drawn around it.
Defaults to 0.04.
interpol : {'linear', 'cubic', 'nearest'}, optional
Interpolation method. This is passed to
scipy.interpolate.griddata for the interpolation of the
Expand Down Expand Up @@ -1417,7 +1433,7 @@ def run(self,
gelpic = gelplot_imshow(distances, bandwidths, intensities, lanes,
names, gel_len, wellx, welly, wellsep, res,
cursor_ovr, back_col, band_col, well_col,
noise, Itol, title, FWTM, False)
noise, Itol, detectlim, title, FWTM, False)
return #gelpic
return None

Expand Down Expand Up @@ -1473,6 +1489,7 @@ def __len__(self):
band_col = 1
well_col = 0.05
noise = 0.5*0.023400015217741609 # 0.015
detectlim = 0.04

# Lane identifiers
lanenames = ['L1', 'S1', 'S2']
Expand Down Expand Up @@ -1519,11 +1536,12 @@ def __len__(self):

# ### Run Gel ###
pic = G.run(till_len, till_time, exposure, plot, res,
cursor_ovr, back_col, band_col, well_col, noise,
cursor_ovr, back_col, band_col, well_col, noise, detectlim,
interpol, dset_name, replNANs)
if plot:
pic.savefig('gelplot.jpg', dpi=300)
pic.show()
# pic.savefig('gelplot.jpg', dpi=300)
# pic.show()
pass

if test_mu0:
# ### Test <ferguson_to_mu0> ### --------------------------------------
Expand Down

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