def test_get_group_colors(self):
"""get_group_colors should iterate over color groups correctly."""
data_colors = color_dict_to_objects(self.data_color_hsv)
exp = (self.colors, data_colors, self.data_color_order)
obs = get_group_colors(self.groups, self.colors, data_colors, self.data_color_order)
self.assertEqual(obs, exp)
def test_get_group_colors(self):
"""get_group_colors should iterate over color groups correctly."""
data_colors = color_dict_to_objects(self.data_color_hsv)
exp = (self.colors, data_colors, self.data_color_order)
obs=get_group_colors(self.groups,self.colors,data_colors,\
self.data_color_order)
self.assertEqual(obs, exp)
def make_all_charts(data,dir_path,filename,num_categories,colorby,args,\
color_data, prefs,background_color,label_color,
chart_type,generate_image_type,plot_width,plot_height,\
bar_width,dpi,resize_nth_label,label_type,\
include_html_legend,include_html_counts):
"""Generate interactive charts in one HTML file"""
#iterate over the preferences and assign colors according to taxonomy
img_data = []
for label,f_name in data:
raw_fpath=os.path.join(dir_path,'raw_data',os.path.split(f_name)[-1])
# move raw file to output directory
shutil.copyfile(f_name,raw_fpath)
f = color_data['counts'][f_name]
level = max([len(t.split(';')) - 1 for t in f[1]])
for key in prefs.keys():
if prefs[key]['column'] != str(level):
continue
col_name = 'Taxon'
mapping = [['Taxon']]
mapping.extend([[m] for m in f[1]])
if 'colors' in prefs[key]:
if isinstance(prefs[key]['colors'], dict):
pref_colors = prefs[key]['colors'].copy()
#copy so we can mutate
else:
pref_colors = prefs[key]['colors'][:]
else:
pref_colors={}
labelname=prefs[key]['column']
#Define groups and associate appropriate colors to each group
groups = group_by_field(mapping, col_name)
pref_colors, data_colors, data_color_order = \
get_group_colors(groups, pref_colors)
updated_pref_colors={}
if chart_type=='area' and len(f[0])==1:
raise ValueError, 'When generating area charts, the number of samples (or category values) must be greater than 1. However, you can still produce a pie chart or bar chart with only 1 sample (or category value), but you must remove the area chart value from the input arguments.'
for key in pref_colors:
updated_pref_colors[key.replace('"','')]=pref_colors[key]
for i,val in enumerate(f[1]):
f[1][i]=val.replace('"','')
#parse the counts and continue processing
img_data.extend(get_counts(label.strip(),colorby,num_categories,\
dir_path,level,f,prefs,updated_pref_colors,\
background_color,\
label_color,chart_type,generate_image_type,\
plot_width,plot_height,bar_width,dpi,raw_fpath,\
resize_nth_label,label_type,include_html_legend,\
include_html_counts))
#generate html filepath
outpath = os.path.join(dir_path,'%s_charts.html' % chart_type)
out_table = ''.join(img_data)
#write out html file
write_html_file(out_table,outpath)
def make_pie_chart(data,
dir_path,
level,
color_data,
prefs,
background_color,
label_color,
file_prefix=None,
props={},
y_len=6.5,
dpi=80,
generate_eps=False,
generate_pdf=True,
others_key="All Other Categories",
others_color="#eeeeee",
should_capitalize=True):
"""
Write interactive piechart
data: [fraction:label,...]
trunc_len: truncates labels after this many chars
"""
if not data:
raise ValueError, "No data available for pie chart."
all_fracs = []
all_labels = []
colors = []
for key in prefs.keys():
if prefs[key]['column'] != str(level):
continue
col_name = 'Taxon'
mapping = [['Taxon']]
mapping.extend([[m] for m in color_data[1]])
if 'colors' in prefs[key]:
if isinstance(prefs[key]['colors'], dict):
pref_colors = prefs[key]['colors'].copy(
) #copy so we can mutate
else:
pref_colors = prefs[key]['colors'][:]
else:
pref_colors = {}
labelname = prefs[key]['column']
#Define groups and associate appropriate colors to each group
groups = group_by_field(mapping, col_name)
pref_colors, data_colors, data_color_order = \
get_group_colors(groups, pref_colors)
# set up labels and colors for pie chart
for color_ix, (c_label, c_frac) in enumerate(data):
#commented out the following line, since the key becomes invalid when
#replacing part of the string.
#c_label = c_label.replace("_", " ")
# we also want to color others category same every time
if c_label == others_key:
colors.append(others_color)
else:
colors.append(data_colors[pref_colors[c_label]].toHex())
all_fracs.append(c_frac)
if should_capitalize:
capital = "%s (%.2f%%)" % (c_label.capitalize(), (c_frac * 100.0))
all_labels.append(capital)
else:
all_labels.append("%s (%.2f%%)" % (c_label, (c_frac * 100.0)))
rc('font', size='10')
rc('text', color=label_color)
rc('patch', linewidth=.1)
rc('axes', linewidth=.5, edgecolor=label_color)
rc('text', usetex=False)
fig = figure(randrange(10000), figsize=(2 * y_len, y_len))
fp = FontProperties()
fp.set_size('8')
if len(data) > 30:
loc = 4
else:
loc = 5
mtitle = "Pie Chart"
if "title" in props:
mtitle = props["title"]
axis('off')
title(mtitle, fontsize='10', color=label_color)
ax = axes([0.0, 0.0, .5, 1])
p1 = pie(all_fracs, shadow=False, colors=colors)
flg = figlegend(p1[0],labels = all_labels, loc = loc, borderpad=0.3, \
labelspacing=0.3, prop = fp)
flg.legendPatch.set_alpha(0.0)
#write out
if file_prefix is None:
img_name = make_img_name()
else:
img_name = file_prefix
img_abs = os.path.join(dir_path, 'pie_charts', img_name)
savefig(img_abs, dpi=dpi, facecolor=background_color)
eps_link = ""
eps_abs = ""
if generate_pdf:
if file_prefix is None:
eps_img_name = make_img_name(file_ext=".pdf")
else:
eps_img_name = file_prefix + ".pdf"
savefig(os.path.join(dir_path, 'pie_charts', eps_img_name),
facecolor=background_color)
eps_abs = os.path.join('pie_charts', eps_img_name)
eps_link = DOWNLOAD_LINK % ((os.path.join('pie_charts',\
eps_img_name)),\
IMG_SRC % (os.path.join('pie_charts',img_name)))
if generate_eps:
if file_prefix is None:
eps_img_name = make_img_name(file_ext=".eps")
else:
eps_img_name = file_prefix + ".eps"
savefig(os.path.join(dir_path, 'pie_charts', eps_img_name),
facecolor=background_color)
strip_eps_font(os.path.join(dir_path, 'pie_charts', eps_img_name))
out = getoutput("gzip " +
os.path.join(dir_path, 'pie_charts', eps_img_name))
eps_abs = os.path.join(dir_path, 'pie_charts', eps_img_name) + ".gz"
eps_link=DOWNLOAD_LINK % ((os.path.join('pie_charts', eps_img_name)+".gz"),\
IMG_SRC % (os.path.join('pie_charts',img_name)))
close(fig)
clf()
return eps_link, IMG_SRC_2 % (os.path.join('pie_charts', img_name))
