def testdata_string(name):
return resource_string(__name__, 'data/' + name, __file__)
def eps_formatter(logodata, format) :
""" Generate a logo in Encapsulated Postscript (EPS)"""
substitutions = {}
from_format =[
"creation_date", "logo_width", "logo_height",
"lines_per_logo", "line_width", "line_height",
"line_margin_right","line_margin_left", "line_margin_bottom",
"line_margin_top", "title_height", "xaxis_label_height",
"creator_text", "logo_title", "logo_margin",
"stroke_width", "tic_length",
"stacks_per_line", "stack_margin",
"yaxis_label", "yaxis_tic_interval", "yaxis_minor_tic_interval",
"xaxis_label", "xaxis_tic_interval", "number_interval",
"fineprint", "shrink_fraction", "errorbar_fraction",
"errorbar_width_fraction",
"errorbar_gray", "small_fontsize", "fontsize",
"title_fontsize", "number_fontsize", "text_font",
"logo_font", "title_font",
"logo_label", "yaxis_scale", "end_type",
"debug", "show_title", "show_xaxis",
"show_xaxis_label", "show_yaxis", "show_yaxis_label",
"show_boxes", "show_errorbars", "show_fineprint",
"rotate_numbers", "show_ends", "stack_height",
"stack_width"
]
for s in from_format :
substitutions[s] = getattr(format,s)
substitutions["shrink"] = str(format.show_boxes).lower()
# --------- COLORS --------------
def format_color(color):
return " ".join( ("[",str(color.red) , str(color.green),
str(color.blue), "]"))
substitutions["default_color"] = format_color(format.default_color)
colors = []
for group in format.color_scheme.groups :
cf = format_color(group.color)
for s in group.symbols :
colors.append( " ("+s+") " + cf )
substitutions["color_dict"] = "\n".join(colors)
data = []
# Unit conversion. 'None' for probability units
conv_factor = std_units[format.unit_name]
data.append("StartLine")
seq_from = format.logo_start- format.first_index
seq_to = format.logo_end - format.first_index +1
# seq_index : zero based index into sequence data
# logo_index : User visible coordinate, first_index based
# stack_index : zero based index of visible stacks
for seq_index in range(seq_from, seq_to) :
logo_index = seq_index + format.first_index
stack_index = seq_index - seq_from
if stack_index!=0 and (stack_index % format.stacks_per_line) ==0 :
data.append("")
data.append("EndLine")
data.append("StartLine")
data.append("")
data.append("(%s) StartStack" % format.annotate[seq_index] )
if conv_factor:
stack_height = logodata.entropy[seq_index] * std_units[format.unit_name]
else :
stack_height = 1.0 # Probability
# Sort by frequency. If equal frequency then reverse alphabetic
# (So sort reverse alphabetic first, then frequencty)
# TODO: doublecheck this actual works
s = list(zip(logodata.counts[seq_index], logodata.alphabet))
s.sort(key= lambda x: x[1])
s.reverse()
s.sort(key= lambda x: x[0])
if not format.reverse_stacks: s.reverse()
C = float(sum(logodata.counts[seq_index]))
if C > 0.0 :
fraction_width = 1.0
if format.scale_width :
fraction_width = logodata.weight[seq_index]
# print(fraction_width, file=sys.stderr)
for c in s:
data.append(" %f %f (%s) ShowSymbol" % (fraction_width, c[0]*stack_height/C, c[1]) )
# Draw error bar on top of logo. Replaced by DrawErrorbarFirst above.
if logodata.entropy_interval is not None and conv_factor and C>0.0:
low, high = logodata.entropy_interval[seq_index]
center = logodata.entropy[seq_index]
low *= conv_factor
high *= conv_factor
center *=conv_factor
if high> format.yaxis_scale : high = format.yaxis_scale
down = (center - low)
up = (high - center)
data.append(" %f %f DrawErrorbar" % (down, up) )
data.append("EndStack")
data.append("")
data.append("EndLine")
substitutions["logo_data"] = "\n".join(data)
# Create and output logo
template = resource_string( __name__, 'template.eps', __file__).decode()
logo = Template(template).substitute(substitutions)
return logo.encode()
def data_string( name ):
"""Load the specified resource as a string."""
fn = _resource_filenames[name]
return resource_string(__name__, fn , __file__)
def data_string(name):
"""Load the specified resource as a string."""
fn = _resource_filenames[name]
return resource_string(__name__, fn, __file__)
def testdata_string( name ):
return resource_string(__name__, 'data/'+name, __file__)
def eps_formatter(logodata, format, fout):
""" Generate a logo in Encapsulated Postscript (EPS)"""
substitutions = {}
from_format = [
"creation_date", "logo_width", "logo_height", "lines_per_logo",
"line_width", "line_height", "line_margin_right", "line_margin_left",
"line_margin_bottom", "line_margin_top", "title_height",
"xaxis_label_height", "creator_text", "logo_title", "logo_margin",
"stroke_width", "tic_length", "stacks_per_line", "stack_margin",
"yaxis_label", "yaxis_tic_interval", "yaxis_minor_tic_interval",
"xaxis_label", "xaxis_tic_interval", "number_interval", "fineprint",
"shrink_fraction", "errorbar_fraction", "errorbar_width_fraction",
"errorbar_gray", "small_fontsize", "fontsize", "title_fontsize",
"number_fontsize", "text_font", "logo_font", "title_font",
"logo_label", "yaxis_scale", "end_type", "debug", "show_title",
"show_xaxis", "show_xaxis_label", "show_yaxis", "show_yaxis_label",
"show_boxes", "show_errorbars", "show_fineprint", "rotate_numbers",
"show_ends", "stack_height", "stack_width", "stack_neg",
"ovline_start", "ovline_end"
]
for s in from_format:
substitutions[s] = getattr(format, s)
substitutions["shrink"] = str(format.show_boxes).lower()
# --------- COLORS --------------
def format_color(color):
return " ".join(
("[", str(color.red), str(color.green), str(color.blue), "]"))
substitutions["default_color"] = format_color(format.default_color)
colors = []
for group in format.color_scheme.groups:
cf = format_color(group.color)
for s in group.symbols:
colors.append(" (" + s + ") " + cf)
substitutions["color_dict"] = "\n".join(colors)
ovline_start, ovline_end = format.ovline_start, format.ovline_end
data = []
# Unit conversion. 'None' for probability units
conv_factor = std_units[format.unit_name]
data.append("StartLine")
seq_from = format.logo_start - format.first_index
seq_to = format.logo_end - format.first_index + 1
# seq_index : zero based index into sequence data
# logo_index : User visible coordinate, first_index based
# stack_index : zero based index of visible stacks
for seq_index in range(seq_from, seq_to):
logo_index = seq_index + format.first_index
stack_index = seq_index - seq_from
if stack_index != 0 and (stack_index % format.stacks_per_line) == 0:
data.append("")
data.append("EndLine")
data.append("StartLine")
data.append("")
data.append("(%s) StartStack" % format.annotate[seq_index])
if conv_factor:
stack_height = logodata.entropy[seq_index] * std_units[
format.unit_name]
else:
stack_height = 1.0 # Probability
s = zip(logodata.counts[seq_index], logodata.alphabet)
def mycmp(c1, c2):
# Sort by frequency. If equal frequency then reverse alphabetic
if c1[0] == c2[0]: return cmp(c2[1], c1[1])
return cmp(c1[0], c2[0])
s.sort(mycmp)
if format.reverse_stacks: s.reverse()
C = float(sum(logodata.counts[seq_index]))
if C > 0.0:
fraction_width = 1.0
## only if you scale the width, we don't do that
## if format.scale_width :
## fraction_width = logodata.weight[seq_index]
# print >>sys.stderr, fraction_width
for c in s:
data.append(" %f %f (%s) ShowSymbol" %
(fraction_width, c[0] * stack_height / C, c[1]))
data.append("EndStack")
if ovline_start <= seq_index <= ovline_end:
data.append("DrawOverline")
data.append("")
data.append("EndLine")
substitutions["logo_data"] = "\n".join(data)
# Create and output logo
template = resource_string(__name__, 'template.eps', __file__)
logo = Template(template).substitute(substitutions)
print >> fout, logo
def eps_formatter( logodata, format, fout, exeSort=True, p_title="P-value") :
""" Generate a logo in Encapsulated Postscript (EPS)"""
substitutions = {}
from_format =[
"creation_date", "logo_width", "logo_height",
"lines_per_logo", "line_width", "line_height",
"line_margin_right","line_margin_left", "line_margin_bottom",
"line_margin_top", "title_height", "xaxis_label_height",
"creator_text", "logo_title", "logo_margin",
"stroke_width", "tic_length",
"stacks_per_line", "stack_margin",
"yaxis_label", "yaxis_tic_interval", "yaxis_minor_tic_interval",
"xaxis_label", "xaxis_tic_interval", "number_interval",
"fineprint", "shrink_fraction", "errorbar_fraction",
"errorbar_width_fraction",
"errorbar_gray", "small_fontsize", "fontsize",
"title_fontsize", "number_fontsize", "text_font",
"logo_font", "title_font",
"logo_label", "yaxis_scale", "end_type",
"debug", "show_title", "show_xaxis",
"show_xaxis_label", "show_yaxis", "show_yaxis_label",
"show_boxes", "show_errorbars", "show_fineprint",
"rotate_numbers", "show_ends", "stack_height",
"stack_width", "show_colorkey"
]
for s in from_format :
substitutions[s] = getattr(format,s)
substitutions["p_title"] = p_title
substitutions["shrink"] = str(format.show_boxes).lower()
# --------- COLORS --------------
def format_color(color):
return " ".join( ("[",str(color.red) , str(color.green),
str(color.blue), "]"))
def choose_color(x, groups):
color = None
d = 1000
for key in groups.keys():
cur_d = abs(abs(key)-abs(x))
if cur_d < d:
d = cur_d
color = groups[key].color
return color
def format_heat_color(col, p_ref, m_ref=None):
heat_colors = []
if m_ref is None:
for c in col:
cf = format_color(choose_color(c[0], p_ref))
heat_colors.append( " ("+c[1]+") " + cf )
else:
for c in col:
if c[0] >= 0:
cf = format_color(choose_color(c[0], p_ref))
else:
cf = format_color(choose_color(c[0], m_ref))
heat_colors.append( " ("+c[1]+") " + cf )
return "\n".join(heat_colors)
plus_ref = {}
minus_ref = {}
p_values = "%\n["
p_colors = " %\n["
for group in format.heat_scheme.groups:
value = float(group.pvalues)
cf = format_color(group.color)
p_values += " ("+group.pvalues+") %\n"
p_colors += cf+" %\n"
if value >= 0:
plus_ref.update( {value:group} )
else:
minus_ref.update( {value:group} )
if len(minus_ref) == 0:
minusref = None
if len(plus_ref) == 0:
plus_ref = minus_ref
minus_ref = None
substitutions["p_values"] = p_values+"]"
substitutions["p_colors"] = p_colors+"]"
substitutions["default_color"] = format_color(format.default_color)
colors = []
if logodata.alphabet in [codon_dna_alphabet, codon_rna_alphabet]:
for group in format.color_scheme.groups :
cf = format_color(group.color)
colors.append( " ("+group.symbols+") " + cf )
else:
for group in format.color_scheme.groups :
cf = format_color(group.color)
for s in group.symbols :
colors.append( " ("+s+") " + cf )
substitutions["color_dict"] = "\n".join(colors)
data = []
# Unit conversion. 'None' for probability units
conv_factor = std_units[format.unit_name]
data.append("StartLine")
seq_from = format.logo_start - format.first_index
seq_to = format.logo_end - format.first_index + 1
# seq_index : zero based index into sequence data
# logo_index : User visible coordinate, first_index based
# stack_index : zero based index of visible stacks
for seq_index in range(seq_from, seq_to) :
logo_index = seq_index + format.first_index
stack_index = seq_index - seq_from
if stack_index!=0 and (stack_index % format.stacks_per_line) ==0 :
data.append("")
data.append("EndLine")
data.append("StartLine")
data.append("")
# color dictionary
if format.make_heatmap == True:
data.append("/color_dict <<")
col = zip(logodata.pvalue[seq_index], logodata.alphabet)
data.append(format_heat_color(col, plus_ref, minus_ref))
data.append(">> def")
data.append("(%s) StartStack" % format.annotate[seq_index] )
if conv_factor:
stack_height = logodata.entropy[seq_index] * std_units[format.unit_name]
else :
stack_height = 1.0 # Probability
s = zip(logodata.counts[seq_index], logodata.alphabet)
def mycmp( c1, c2 ) :
# Sort by frequency. If equal frequency then reverse alphabetic
if c1[0] == c2[0] : return cmp(c2[1], c1[1])
return cmp(c1[0], c2[0])
if exeSort: s.sort(mycmp)
if not format.reverse_stacks: s.reverse()
C = float(sum(logodata.counts[seq_index]))
if C > 0.0 :
fraction_width = 1.0
if format.scale_width :
fraction_width = logodata.weight[seq_index]
# print >>sys.stderr, fraction_width
for c in s:
data.append(" %f %f (%s) ShowSymbol" % (fraction_width, c[0]*stack_height/C, c[1]) )
# Draw error bar on top of logo. Replaced by DrawErrorbarFirst above.
if logodata.entropy_interval is not None and conv_factor and C>0.0:
low, high = logodata.entropy_interval[seq_index]
center = logodata.entropy[seq_index]
low *= conv_factor
high *= conv_factor
center *=conv_factor
if high> format.yaxis_scale : high = format.yaxis_scale
down = (center - low)
up = (high - center)
data.append(" %f %f DrawErrorbar" % (down, up) )
data.append("EndStack")
data.append("")
data.append("EndLine")
substitutions["logo_data"] = "\n".join(data)
# Create and output logo
template = resource_string( __name__, 'template.eps', __file__)
logo = Template(template).substitute(substitutions)
print >>fout, logo
