def plot_density_from_file(settings_f,
pickle_filename,
event,
output_dir,
no_posteriors=False,
plot_title=None,
plot_label=None):
"""
Read MISO estimates given an event name.
"""
##
## Read information about gene
##
tx_start, tx_end, exon_starts, exon_ends, gene_obj, mRNAs, strand, chrom = \
parseGene(pickle_filename, event)
# check the output format
is_png = False
if plot_label is not None:
if plot_label[-4:] == ".png":
is_png = True
plot_label = plot_label[:-4]
elif plot_label[-4:] == ".pdf":
plot_label = plot_label[:-4]
# Override settings flag on whether to show posterior plots
# if --no-posteriors was given to plot.py
sashimi_obj = Sashimi(event,
output_dir,
event=event,
chrom=chrom,
settings_filename=settings_f,
no_posteriors=no_posteriors,
png=is_png)
print "Plotting read densities and MISO estimates along event..."
print " - Event: %s" % (event)
settings = sashimi_obj.settings
if no_posteriors:
settings["show_posteriors"] = False
bam_files = settings['bam_files']
miso_files = settings['miso_files']
# Setup the figure
sashimi_obj.setup_figure()
plot_density(sashimi_obj, pickle_filename, event, plot_title=plot_title)
# Save figure
sashimi_obj.save_plot(plot_label=plot_label)
def plot_density_from_file(settings_f, pickle_filename, event,
output_dir,
no_posteriors=False,
plot_title=None,
plot_label=None):
"""
Read MISO estimates given an event name.
"""
##
## Read information about gene
##
tx_start, tx_end, exon_starts, exon_ends, gene_obj, mRNAs, strand, chrom = \
parseGene(pickle_filename, event)
#chrom = str(chrom)[3:]
# Override settings flag on whether to show posterior plots
# if --no-posteriors was given to plot.py
sashimi_obj = Sashimi(event, output_dir,
event=event,
chrom=chrom,
settings_filename=settings_f,
no_posteriors=no_posteriors)
#print "Plotting read densities and MISO estimates along event..."
#print " - Event: %s" %(event)
settings = sashimi_obj.settings
if no_posteriors:
settings["show_posteriors"] = False
bam_files = settings['bam_files']
miso_files = settings['miso_files']
# Setup the figure
sashimi_obj.setup_figure()
plot_density(sashimi_obj, pickle_filename, event,
plot_title=plot_title)
# Save figure
sashimi_obj.save_plot(plot_label=plot_label)
def plot_density(sashimi_obj, pickle_filename, event, plot_title=None, group_info=None):
# intron_scale=30, exon_scale=1, gene_posterior_ratio=5, posterior_bins=40,
# colors=None, ymax=None, logged=False, show_posteriors=True, coverages=None,
# number_junctions=True, resolution=.5, fig_width=8.5, fig_height=11,
# font_size=6, junction_log_base=10, reverse_minus=False,
# bar_posterior=False):
# Get the settings we need
settings = sashimi_obj.settings
bam_files = settings["bam_files"]
miso_files = settings["miso_files"]
intron_scale = settings["intron_scale"]
exon_scale = settings["exon_scale"]
gene_posterior_ratio = settings["gene_posterior_ratio"]
posterior_bins = settings["posterior_bins"]
colors = settings["colors"]
ymax = settings["ymax"]
logged = settings["logged"]
show_posteriors = settings["show_posteriors"]
coverages = settings["coverages"]
number_junctions = settings["number_junctions"]
resolution = settings["resolution"]
junction_log_base = settings["junction_log_base"]
reverse_minus = settings["reverse_minus"]
bar_posterior = settings["bar_posteriors"]
font_size = settings["font_size"]
nyticks = settings["nyticks"]
nxticks = settings["nxticks"]
show_ylabel = settings["show_ylabel"]
show_xlabel = settings["show_xlabel"]
if plot_title is None:
plot_title = event
print "Using intron scale ", intron_scale
print "Using exon scale ", exon_scale
# Always show y-axis for read densities for now
showYaxis = True
# Parse gene pickle file to get information about gene
tx_start, tx_end, exon_starts, exon_ends, gene_obj, mRNAs, strand, chrom = \
parseGene(pickle_filename, event)
# Get the right scalings
graphcoords, graphToGene = getScaling(tx_start, tx_end, strand,
exon_starts, exon_ends, intron_scale,
exon_scale, reverse_minus)
if group_info is not None:
group_files, group_labels, group_colors = analyze_group_info(group_info, bam_files, settings["sample_labels"])
settings["sample_labels"] = group_labels
# if the group color is customized by the user
if len(colors) != len(group_colors):
print('\033[0;31;m') # change the print color as red
print("The number of custom colors is {0} which doesn't match the group number {1}. The program uses the "
"rainbow color as default.".format(len(colors), len(group_colors)))
print('\033[0m') # set the color as default value
colors = settings["colors"] = group_colors
nfiles = len(group_files)
else:
nfiles = len(bam_files)
group_files = []
# if the group_info is not provided, also produce a group_file = [['bam1'],['bam2'],...]
for i in range(nfiles):
group_files.append([bam_files[i]])
if plot_title is not None:
# Use custom title if given
suptitle(plot_title, fontsize=10)
else:
suptitle(event, fontsize=10)
plotted_axes = []
maxys = np.zeros(nfiles)
for i in range(nfiles):
if colors is not None:
color = colors[i]
else:
color = None
if coverages is not None:
coverage = coverages[i]
else:
coverage = 1
if i < nfiles - 1:
showXaxis = False
else:
showXaxis = True
bam_group = group_files[i] # ['./testData/S1.R1.test.bam','./testData/S1.R2.test.bam']
# bam_file = os.path.expanduser(bam_files[i])
ax1 = subplot2grid((nfiles + 3, gene_posterior_ratio), (i, 0),
colspan=gene_posterior_ratio - 1)
# Read sample label
sample_label = settings["sample_labels"][i]
print "Reading sample label: %s" %(sample_label)
# print "Processing BAM: %s" %(bam_file)
plotted_ax, maxy = plot_density_single(settings, sample_label,
tx_start, tx_end, gene_obj, mRNAs, strand,
graphcoords, graphToGene, bam_group, ax1, chrom,
paired_end=False, intron_scale=intron_scale,
exon_scale=exon_scale, color=color,
ymax=ymax, logged=logged, coverage=coverage,
number_junctions=number_junctions, resolution=resolution,
showXaxis=showXaxis, nyticks=nyticks, nxticks=nxticks,
show_ylabel=show_ylabel, show_xlabel=show_xlabel,
font_size=font_size,
junction_log_base=junction_log_base)
plotted_axes.append(plotted_ax)
maxys[i] = maxy
if show_posteriors:
miso_file = os.path.expanduser(miso_files[i])
try:
ax2 = subplot2grid((nfiles + 3, gene_posterior_ratio),\
(i, gene_posterior_ratio - 1))
if not os.path.isfile(miso_file):
print "Warning: MISO file %s not found" %(miso_file)
print "Loading MISO file: %s" %(miso_file)
plot_posterior_single(miso_file, ax2, posterior_bins,
showXaxis=showXaxis, show_ylabel=False,
font_size=font_size,
bar_posterior=bar_posterior)
except:
box(on=False)
xticks([])
yticks([])
print "Posterior plot failed."
##
## Figure out correct y-axis values
##
ymax_vals = []
if ymax != None:
# Use user-given ymax values if provided
max_used_yval = ymax
else:
# Compute best ymax value for all samples: take
# maximum y across all.
used_yvals = [curr_ax.get_ylim()[1] for curr_ax in plotted_axes]
# Round up
max_used_yval = math.ceil(max(used_yvals))
# Reset axes based on this.
# Set fake ymin bound to allow lower junctions to be visible
fake_ymin = -0.6 * max_used_yval
universal_yticks = linspace(0, max_used_yval,
nyticks + 1)
# Round up yticks
universal_ticks = map(math.ceil, universal_yticks)
for sample_num, curr_ax in enumerate(plotted_axes):
if showYaxis:
curr_ax.set_ybound(lower=fake_ymin, upper=max_used_yval)
curr_yticklabels = []
for label in universal_yticks:
if label <= 0:
# Exclude label for 0
curr_yticklabels.append("")
else:
if label % 1 != 0:
curr_yticklabels.append("%.1f" %(label))
else:
curr_yticklabels.append("%d" %(label))
curr_ax.set_yticklabels(curr_yticklabels,
fontsize=font_size)
curr_ax.spines["left"].set_bounds(0, max_used_yval)
curr_ax.set_yticks(universal_yticks)
curr_ax.yaxis.set_ticks_position('left')
curr_ax.spines["right"].set_color('none')
if show_ylabel:
y_horz_alignment = 'left'
if logged:
curr_ax.set_ylabel('RPKM $(\mathregular{\log}_{\mathregular{10}})$',
fontsize=font_size,
ha=y_horz_alignment)
else:
curr_ax.set_ylabel('RPKM',
fontsize=font_size,
va="bottom",
ha=y_horz_alignment)
else:
curr_ax.spines["left"].set_color('none')
curr_ax.spines["right"].set_color('none')
curr.ax.set_yticks([])
##
## Plot sample labels
##
sample_color = colors[sample_num]
# Make sample label y position be halfway between highest
# and next to highest ytick
if len(universal_yticks) >= 2:
halfway_ypos = (universal_yticks[-1] - universal_yticks[-2]) / 2.
label_ypos = universal_yticks[-2] + halfway_ypos
else:
label_ypos = universal_yticks[-1]
curr_label = settings["sample_labels"][sample_num]
curr_ax.text(max(graphcoords), max(label_ypos, maxys[sample_num]),
curr_label,
fontsize=font_size,
va='bottom',
ha='right',
color=sample_color)
# Draw gene structure
ax = subplot2grid((nfiles + 3, gene_posterior_ratio), (nfiles + 1, 0),
colspan=gene_posterior_ratio - 1, rowspan=2)
plot_mRNAs(tx_start, mRNAs, strand, graphcoords, reverse_minus)
subplots_adjust(hspace=.10, wspace=.7)
def plot_density(sashimi_obj, pickle_filename, event, plot_title=None):
# intron_scale=30, exon_scale=1, gene_posterior_ratio=5, posterior_bins=40,
# colors=None, ymax=None, logged=False, show_posteriors=True, coverages=None,
# number_junctions=True, resolution=.5, fig_width=8.5, fig_height=11,
# font_size=6, junction_log_base=10, reverse_minus=False,
# bar_posterior=False):
# Get the settings we need
settings = sashimi_obj.settings
bam_files = settings["bam_files"]
miso_files = settings["miso_files"]
intron_scale = settings["intron_scale"]
exon_scale = settings["exon_scale"]
gene_posterior_ratio = settings["gene_posterior_ratio"]
posterior_bins = settings["posterior_bins"]
colors = settings["colors"]
ymax = settings["ymax"]
logged = settings["logged"]
show_posteriors = settings["show_posteriors"]
coverages = settings["coverages"]
number_junctions = settings["number_junctions"]
resolution = settings["resolution"]
junction_log_base = settings["junction_log_base"]
reverse_minus = settings["reverse_minus"]
bar_posterior = settings["bar_posteriors"]
font_size = settings["font_size"]
nyticks = settings["nyticks"]
nxticks = settings["nxticks"]
show_ylabel = settings["show_ylabel"]
show_xlabel = settings["show_xlabel"]
if plot_title is None:
plot_title = event
print "Using intron scale ", intron_scale
print "Using exon scale ", exon_scale
# Always show y-axis for read densities for now
showYaxis = True
# Parse gene pickle file to get information about gene
tx_start, tx_end, exon_starts, exon_ends, gene_obj, mRNAs, strand, chrom = \
parseGene(pickle_filename, event)
# Get the right scalings
graphcoords, graphToGene = getScaling(tx_start, tx_end, strand,
exon_starts, exon_ends, intron_scale,
exon_scale, reverse_minus)
nfiles = len(bam_files)
if plot_title is not None:
# Use custom title if given
suptitle(plot_title, fontsize=10)
else:
suptitle(event, fontsize=10)
plotted_axes = []
for i in range(nfiles):
if colors is not None:
color = colors[i]
else:
color = None
if coverages is not None:
coverage = coverages[i]
else:
coverage = 1
if i < nfiles - 1:
showXaxis = False
else:
showXaxis = True
bam_file = os.path.expanduser(bam_files[i])
ax1 = subplot2grid((nfiles + 3, gene_posterior_ratio), (i, 0),
colspan=gene_posterior_ratio - 1)
# Read sample label
sample_label = settings["sample_labels"][i]
print "Reading sample label: %s" %(sample_label)
print "Processing BAM: %s" %(bam_file)
plotted_ax = plot_density_single(settings, sample_label,
tx_start, tx_end, gene_obj, mRNAs, strand,
graphcoords, graphToGene, bam_file, ax1, chrom,
paired_end=False, intron_scale=intron_scale,
exon_scale=exon_scale, color=color,
ymax=ymax, logged=logged, coverage=coverage,
number_junctions=number_junctions, resolution=resolution,
showXaxis=showXaxis, nyticks=nyticks, nxticks=nxticks,
show_ylabel=show_ylabel, show_xlabel=show_xlabel,
font_size=font_size,
junction_log_base=junction_log_base)
plotted_axes.append(plotted_ax)
if show_posteriors:
miso_file = os.path.expanduser(miso_files[i])
try:
ax2 = subplot2grid((nfiles + 3, gene_posterior_ratio),\
(i, gene_posterior_ratio - 1))
if not os.path.isfile(miso_file):
print "Warning: MISO file %s not found" %(miso_file)
print "Loading MISO file: %s" %(miso_file)
plot_posterior_single(miso_file, ax2, posterior_bins,
showXaxis=showXaxis, show_ylabel=False,
font_size=font_size,
bar_posterior=bar_posterior)
except:
box(on=False)
xticks([])
yticks([])
print "Posterior plot failed."
##
## Figure out correct y-axis values
##
ymax_vals = []
if ymax != None:
# Use user-given ymax values if provided
max_used_yval = ymax
else:
# Compute best ymax value for all samples: take
# maximum y across all.
used_yvals = [curr_ax.get_ylim()[1] for curr_ax in plotted_axes]
# Round up
max_used_yval = math.ceil(max(used_yvals))
# Reset axes based on this.
# Set fake ymin bound to allow lower junctions to be visible
fake_ymin = -0.6 * max_used_yval
universal_yticks = linspace(0, max_used_yval,
nyticks + 1)
# Round up yticks
universal_ticks = map(math.ceil, universal_yticks)
for sample_num, curr_ax in enumerate(plotted_axes):
if showYaxis:
curr_ax.set_ybound(lower=fake_ymin, upper=max_used_yval)
curr_yticklabels = []
for label in universal_yticks:
if label <= 0:
# Exclude label for 0
curr_yticklabels.append("")
else:
if label % 1 != 0:
curr_yticklabels.append("%.1f" %(label))
else:
curr_yticklabels.append("%d" %(label))
curr_ax.set_yticklabels(curr_yticklabels,
fontsize=font_size)
curr_ax.spines["left"].set_bounds(0, max_used_yval)
curr_ax.set_yticks(universal_yticks)
curr_ax.yaxis.set_ticks_position('left')
curr_ax.spines["right"].set_color('none')
if show_ylabel:
y_horz_alignment = 'left'
if logged:
curr_ax.set_ylabel('RPKM $(\mathregular{\log}_{\mathregular{10}})$',
fontsize=font_size,
ha=y_horz_alignment)
else:
curr_ax.set_ylabel('RPKM',
fontsize=font_size,
va="bottom",
ha=y_horz_alignment)
else:
curr_ax.spines["left"].set_color('none')
curr_ax.spines["right"].set_color('none')
curr.ax.set_yticks([])
##
## Plot sample labels
##
sample_color = colors[sample_num]
# Make sample label y position be halfway between highest
# and next to highest ytick
if len(universal_yticks) >= 2:
halfway_ypos = (universal_yticks[-1] - universal_yticks[-2]) / 2.
label_ypos = universal_yticks[-2] + halfway_ypos
else:
label_ypos = universal_yticks[-1]
curr_label = settings["sample_labels"][sample_num]
curr_ax.text(max(graphcoords), label_ypos,
curr_label,
fontsize=font_size,
va='bottom',
ha='right',
color=sample_color)
# Draw gene structure
ax = subplot2grid((nfiles + 3, gene_posterior_ratio), (nfiles + 1, 0),
colspan=gene_posterior_ratio - 1, rowspan=2)
plot_mRNAs(tx_start, mRNAs, strand, graphcoords, reverse_minus)
subplots_adjust(hspace=.10, wspace=.7)
def plot_density(sashimi_obj, pickle_filename, event, plot_title=None):
# intron_scale=30, exon_scale=1, gene_posterior_ratio=5, posterior_bins=40,
# colors=None, ymax=None, logged=False, show_posteriors=True, coverages=None,
# number_junctions=True, resolution=.5, fig_width=8.5, fig_height=11,
# font_size=6, junction_log_base=10, reverse_minus=False,
# bar_posterior=False):
# Get the settings we need
settings = sashimi_obj.settings
bam_files = settings["bam_files"]
miso_files = settings["miso_files"]
intron_scale = settings["intron_scale"]
exon_scale = settings["exon_scale"]
gene_posterior_ratio = settings["gene_posterior_ratio"]
posterior_bins = settings["posterior_bins"]
colors = settings["colors"]
ymax = settings["ymax"]
logged = settings["logged"]
show_posteriors = settings["show_posteriors"]
coverages = settings["coverages"]
number_junctions = settings["number_junctions"]
resolution = settings["resolution"]
junction_log_base = settings["junction_log_base"]
reverse_minus = settings["reverse_minus"]
bar_posterior = settings["bar_posteriors"]
font_size = settings["font_size"]
nyticks = settings["nyticks"]
nxticks = settings["nxticks"]
show_ylabel = settings["show_ylabel"]
show_xlabel = settings["show_xlabel"]
if plot_title is None:
plot_title = event
print "Using intron scale ", intron_scale
print "Using exon scale ", exon_scale
# Always show y-axis for read densities for now
showYaxis = True
# Parse gene pickle file to get information about gene
tx_start, tx_end, exon_starts, exon_ends, gene_obj, mRNAs, strand, chrom = \
parseGene(pickle_filename, event)
# Get the right scalings
graphcoords, graphToGene = getScaling(tx_start, tx_end, strand,
exon_starts, exon_ends, intron_scale,
exon_scale, reverse_minus)
nfiles = len(bam_files)
if plot_title is not None:
# Use custom title if given
suptitle(plot_title, fontsize=1.4 * font_size)
else:
suptitle(event, fontsize=1.4 * font_size)
plotted_axes = []
h_ratio = [1] * nfiles + [font_size / 10.0, len(mRNAs) * 0.25]
if show_posteriors:
w_ratio = [gene_posterior_ratio, 1]
gs = gridspec.GridSpec(nfiles + 2,
2,
height_ratios=h_ratio,
width_ratios=w_ratio)
else:
gs = gridspec.GridSpec(nfiles + 2, 1, height_ratios=h_ratio)
for i in range(nfiles):
if colors is not None:
color = colors[i]
else:
color = None
if coverages is not None:
coverage = coverages[i]
else:
coverage = 1
if i < nfiles - 1:
showXaxis = False
else:
showXaxis = True
bam_file = os.path.expanduser(bam_files[i])
# Read sample label
sample_label = settings["sample_labels"][i]
print "Reading sample label: %s" % (sample_label)
print "Processing BAM: %s" % (bam_file)
ax1 = subplot(gs[i, 0])
plotted_ax = plot_density_single(settings,
sample_label,
tx_start,
tx_end,
gene_obj,
mRNAs,
strand,
graphcoords,
graphToGene,
bam_file,
ax1,
chrom,
paired_end=False,
intron_scale=intron_scale,
exon_scale=exon_scale,
color=color,
ymax=ymax,
logged=logged,
coverage=coverage,
number_junctions=number_junctions,
resolution=resolution,
showXaxis=showXaxis,
nyticks=nyticks,
nxticks=nxticks,
show_ylabel=show_ylabel,
show_xlabel=show_xlabel,
font_size=font_size,
junction_log_base=junction_log_base)
plotted_axes.append(plotted_ax)
if show_posteriors:
miso_file = os.path.expanduser(miso_files[i])
try:
ax2 = subplot(gs[i, 1])
if not os.path.isfile(miso_file):
print "Warning: MISO file %s not found" % (miso_file)
print "Loading MISO file: %s" % (miso_file)
plot_posterior_single(miso_file,
ax2,
posterior_bins,
event,
showXaxis=showXaxis,
show_ylabel=False,
font_size=font_size,
bar_posterior=bar_posterior)
except:
box(on=False)
xticks([])
yticks([])
print "Posterior plot failed."
##
## Figure out correct y-axis values
##
ymax_vals = []
if ymax != None:
# Use user-given ymax values if provided
max_used_yval = ymax
else:
# Compute best ymax value for all samples: take
# maximum y across all.
used_yvals = [curr_ax.get_ylim()[1] for curr_ax in plotted_axes]
# Round up
max_used_yval = max(used_yvals) * 1.05 // nyticks * nyticks
# Reset axes based on this.
# Set fake ymin bound to allow lower junctions to be visible
fake_ymin = -0.6 * max_used_yval
universal_yticks = linspace(0, max_used_yval, nyticks + 1)
# Round up yticks
universal_ticks = map(math.ceil, universal_yticks)
for sample_num, curr_ax in enumerate(plotted_axes):
if showYaxis:
curr_ax.set_ybound(lower=fake_ymin, upper=max_used_yval)
curr_yticklabels = []
for label in universal_yticks:
if label <= 0:
# Exclude label for 0
curr_yticklabels.append("")
else:
if label % 1 != 0:
curr_yticklabels.append("%.1f" % (label))
else:
curr_yticklabels.append("%d" % (label))
curr_ax.set_yticklabels(curr_yticklabels, fontsize=font_size)
curr_ax.spines["left"].set_bounds(0, max_used_yval)
curr_ax.set_yticks(universal_yticks)
curr_ax.yaxis.set_ticks_position('left')
curr_ax.spines["right"].set_color('none')
if show_ylabel and sample_num == nfiles // 2:
y_horz_alignment = 'left'
if logged:
curr_ax.set_ylabel(
'RPKM $(\mathregular{\log}_{\mathregular{10}})$',
fontsize=font_size,
ha=y_horz_alignment)
else:
curr_ax.set_ylabel('RPKM',
fontsize=font_size,
va="bottom",
ha=y_horz_alignment)
else:
curr_ax.spines["left"].set_color('none')
curr_ax.spines["right"].set_color('none')
curr.ax.set_yticks([])
##
## Plot sample labels
##
sample_color = colors[sample_num]
# Make sample label y position be halfway between highest
# and next to highest ytick
if len(universal_yticks) >= 2:
halfway_ypos = (universal_yticks[-1] - universal_yticks[-2]) / 2.
label_ypos = universal_yticks[-2] + halfway_ypos
else:
label_ypos = universal_yticks[-1]
curr_label = settings["sample_labels"][sample_num]
curr_ax.text(max(graphcoords),
label_ypos,
curr_label,
fontsize=font_size * 1.2,
va='bottom',
ha='right',
color=sample_color)
# Draw gene structure
ax = subplot(gs[nfiles + 1, 0])
plot_mRNAs(tx_start, mRNAs, strand, graphcoords, reverse_minus)
# subplots_adjust(hspace=.10, wspace=.7)
subplots_adjust(hspace=.0, wspace=0.1)
