def _load_data(self, interval):
self.gene_track = load_annotation(interval,
self.annofile,
vis=self.vis)
self.max_tracks = len(self.gene_track.keys())
self.height *= self.max_tracks
def _load_data(self, interval):
self.gene_track = load_annotation(interval, self.annofile, vis=self.vis)
self.max_tracks = len(list(self.gene_track.keys()))
self.height *= self.max_tracks
def profile_screenshot(fname,
interval,
tracks,
fontsize=None,
colors=None,
scalegroups=None,
scale=None,
show_scale=True,
annotation=None,
bgmode="color",
fragmentsize=200,
dpi=600,
rmdup=False,
rmrepeats=False,
reverse=False,
adjscale=False):
"""
Plot a genome browser like profile
Parameters
----------
fname: string
output file name
interval: string
interval to plot in "chrom:start-end" format
tracks: list
list of filenames
"""
if scalegroups is None:
scalegroups = []
if not fontsize:
fontsize = FONTSIZE
if not colors:
colors = DEFAULT_COLORS
# Plot size and padding definition
plotwidth = 6
plotheight = 0.3
pad = {
"left": 1.5,
"right": 0.05,
"top": 0.05,
"bottom": 0.05,
"row": 0,
"column": 3,
}
# adjust width for track names if they are to long
# kind of a quick hack
max_len = 0
for group in tracks:
names = [
os.path.splitext(os.path.basename(t))[0].strip() for t in group
]
l = sum([len(name) for name in names])
if l > max_len:
max_len = l
if max_len > 27:
pad["left"] = 3
# Genomic scale
scale_height = 0.1
# Annotation track height
annotation_height = 0.01
chrom, start, end = re.split(r'[-:]', interval)
start, end = int(start), int(end)
if annotation:
ann = load_annotation([chrom, start, end], annotation)
if ann:
annotation_height = 0.2 * len(ann.keys())
else:
annotation = False
nrows = len(tracks)
wsize = pad["left"] + plotwidth + pad["right"]
hsize = pad["top"] + (nrows * plotheight) + (pad["row"] *
(nrows - 1)) + pad["bottom"]
hsize += scale_height + pad["row"] + annotation_height + pad["row"]
# initialize figure
fig = plt.figure(figsize=(wsize, hsize))
# initialize profile figure
pfig = ProfileFigure(fig=fig, fontsize=fontsize, pad=pad)
# add the genomic scale
pfig.add_panel(ScalePanel())
if type(scale) != type([]):
scale = [scale]
# add the signal tracks
c = 0
for group in tracks:
for i, track in enumerate(group):
panel = pfig.add_panel(BamProfilePanel(
track,
color=colors[c % len(colors)],
bgmode=bgmode,
name=os.path.splitext(os.path.split(track)[-1])[0],
fragmentsize=fragmentsize,
rmrepeats=rmrepeats,
rmdup=rmdup,
adjscale=adjscale,
show_scale=show_scale,
),
overlay=i != 0)
panel.ymax = scale[c % len(scale)]
c += 1
# add the annotation panel
if annotation:
pfig.add_panel(AnnotationPanel(annotation))
pfig.plot([chrom, start, end], scalegroups=scalegroups, reverse=reverse)
plt.savefig(fname, dpi=dpi)
def profile_screenshot(fname, interval, tracks, fontsize=None, colors=None, scalegroups=None, scale=None, show_scale=True, annotation=None, bgmode="color", fragmentsize=200, dpi=600, rmdup=False, rmrepeats=False, reverse=False, adjscale=False):
"""
Plot a genome browser like profile
Parameters
----------
fname: string
output file name
interval: string
interval to plot in "chrom:start-end" format
tracks: list
list of filenames
"""
if scalegroups is None:
scalegroups = []
if not fontsize:
fontsize = FONTSIZE
if not colors:
colors = DEFAULT_COLORS
# Plot size and padding definition
plotwidth = 6
plotheight = 0.3
pad = {
"left": 1.5,
"right": 0.05,
"top": 0.05,
"bottom": 0.05,
"row": 0,
"column": 3,
}
# adjust width for track names if they are to long
# kind of a quick hack
max_len = 0
for group in tracks:
names = [os.path.splitext(os.path.basename(t))[0].strip() for t in group]
l = sum([len(name) for name in names])
if l > max_len:
max_len = l
if max_len > 27:
pad["left"] = 3
# Genomic scale
scale_height = 0.1
# Annotation track height
annotation_height = 0.01
chrom, start, end = re.split(r'[-:]', interval)
start, end = int(start), int(end)
if annotation:
ann = load_annotation([chrom,start,end], annotation)
if ann:
annotation_height = 0.2 * len(list(ann.keys()))
else:
annotation = False
nrows = len(tracks)
wsize = pad["left"] + plotwidth + pad["right"]
hsize = pad["top"] + (nrows * plotheight) + (pad["row"] * (nrows - 1)) + pad["bottom"]
hsize += scale_height + pad["row"] + annotation_height + pad["row"]
# initialize figure
fig = plt.figure(figsize=(wsize, hsize))
# initialize profile figure
pfig = ProfileFigure(fig=fig, fontsize=fontsize, pad=pad)
# add the genomic scale
pfig.add_panel(ScalePanel())
if type(scale) != type([]):
scale = [scale]
# add the signal tracks
c = 0
for group in tracks:
for i,track in enumerate(group):
panel = pfig.add_panel(
BamProfilePanel(track,
color = colors[c % len(colors)],
bgmode = bgmode,
name = os.path.splitext(os.path.split(track)[-1])[0],
fragmentsize = fragmentsize,
rmrepeats = rmrepeats,
rmdup = rmdup,
adjscale = adjscale,
show_scale = show_scale,
),
overlay= i != 0
)
panel.ymax = scale[c % len(scale)]
c += 1
# add the annotation panel
if annotation:
pfig.add_panel(AnnotationPanel(annotation))
pfig.plot([chrom, start, end], scalegroups=scalegroups, reverse=reverse)
plt.savefig(fname, dpi=dpi)
