generated from bartonlab/paper-template
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mplot.py
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mplot.py
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"""
Minimal plotting functions implemented through matplotlib.
"""
############# PACKAGES #############
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
#matplotlib.rcParams['pdf.fonttype'] = 42
from matplotlib.ticker import FixedLocator
from scipy.stats.kde import gaussian_kde
from copy import deepcopy
############# PARAMETERS #############
#matplotlib.rcParams['pdf.fonttype'] = 42
blues = {
3 : ['#3182bd', '#9ecae1', '#deebf7'],
4 : ['#525252', '#969696', '#cccccc', '#f7f7f7'],
5 : ['#252525', '#636363', '#969696', '#cccccc', '#f7f7f7'],
6 : ['#252525', '#636363', '#969696', '#bdbdbd', '#d9d9d9', '#f7f7f7'],
7 : ['#252525', '#525252', '#737373', '#969696', '#bdbdbd', '#d9d9d9', '#f7f7f7'],
8 : ['#252525', '#525252', '#737373', '#969696', '#bdbdbd', '#d9d9d9', '#f0f0f0', '#ffffff']
}
greys = {
3 : ['#636363', '#bdbdbd', '#f0f0f0'],
4 : ['#2171b5', '#6baed6', '#bdd7e7', '#eff3ff'],
5 : ['#08519c', '#3182bd', '#6baed6', '#bdd7e7', '#eff3ff'],
6 : ['#08519c', '#3182bd', '#6baed6', '#9ecae1', '#c6dbef', '#eff3ff'],
7 : ['#084594', '#2171b5', '#4292c6', '#6baed6', '#9ecae1', '#c6dbef', '#eff3ff'],
8 : ['#084594', '#2171b5', '#4292c6', '#6baed6', '#9ecae1', '#c6dbef', '#deebf7', '#f7fbff']
}
defcolor = '#252525'
defplotcolor = '#2171b5'
defpaircolor = ['#2171b5', '#9ecae1']
def cm2inch(x): return float(x)/2.54
goldr = (1.0 + np.sqrt(5)) / 2.0
nbins = 50
aspect = 1.0
plotwidth = cm2inch(8.90)
offset = 0.02
offsetpt = 1.0
sublabelx = -0.10
sublabely = 0.95
ticklength = 3
tickpad = 3
axwidth = 0.4
sizedot = 8.
sizeline = 0.8
textcolor = defcolor
# paper
fontfamily = 'Arial'
sizesublabel = 8+1
sizetext = 6
sizelabel = 6
sizetick = 6
smallsizedot = 6
## grant
#fontfamily = 'Arial'
#sizesublabel = 12
#sizetext = 8
#sizelabel = 8
#sizetick = 8
#smallsizedot = 6. * 2
#sizeline = 1
# # slides/poster
# fontfamily = 'Avenir'
# sizesublabel = 18
# sizetext = 18
# sizelabel = 18
# sizetick = 18
# smallsizedot = 6. * 4
# axwidth = 1.5
# sizeline = 2.0
def_labelprops = {
'family' : fontfamily,
'size' : sizelabel,
'color' : textcolor
}
def_sublabelprops = {
'family' : fontfamily,
'size' : sizesublabel,
'weight' : 'bold',
'ha' : 'center',
'va' : 'center',
'color' : 'k'
}
def_ticklabelprops = {
'family' : fontfamily,
'size' : sizetick,
'color' : textcolor
}
def_axprops = {
'linewidth' : axwidth,
'linestyle' : '-',
'color' : textcolor
}
def_tickprops = {
'length' : ticklength,
'width' : axwidth/2,
'pad' : tickpad,
'axis' : 'both',
'direction' : 'out',
'colors' : textcolor,
'bottom' : True,
'left' : True,
'top' : False,
'right' : False
}
def_minortickprops = {
'length' : ticklength-1.25,
'width' : axwidth/2,
'axis' : 'both',
'direction' : 'out',
'which' : 'minor',
'colors' : textcolor
}
def_legendprops = {
'loc' : 1,
'frameon' : False,
'scatterpoints' : 1,
'handletextpad' : -0.1,
'prop' : {'size' : sizelabel}
}
def_scatterprops = {
'lw' : 0,
's' : sizedot,
'marker' : 'o'
}
# Define a new function "callout" which circles points on a scatter plot and labels them
# Need properties for the arrows, the scatter points, and the text
def_callscatterprops = {
'lw' : sizeline,
's' : sizedot,
'marker' : 'o'
}
def_callarrowprops = {
'lw' : sizeline,
's' : sizedot,
'marker' : 'o'
}
def_errorprops = {
'mew' : 0,
'markersize' : smallsizedot/2,
'fmt' : 'o',
'elinewidth' : sizeline/2,
'capthick' : 0,
'capsize' : 0
}
def_lineprops = {
'lw' : sizeline,
'ls' : '-',
#'drawstyle' : 'steps'
}
def_fillprops = {
'lw' : sizeline,
'linestyle' : '-',
'interpolate' : True
}
# NEW STYLE SOLID
def_histprops = {
'histtype' : 'bar',
'lw' : sizeline/2,
'ls' : 'solid',
'edgecolor' : defcolor,
'align' : 'left'
}
# OLD STYLE OUTLINE
#def_histprops = {
# 'histtype' : 'step',#'bar',
# 'lw' : sizeline,#/2,
# 'ls' : 'solid',
# #'edgecolor' : defcolor
# }
def_barprops = {
'lw' : sizeline/2,
'width' : 1,
'edgecolor' : defcolor,
'align' : 'center', #other option: edge
'orientation' : 'vertical'
}
def_violinprops = {
'vert' : False,
'widths' : 0.5, # Maximum height for violin, ~ half of vertical space
'showmeans' : True,
'showextrema' : False,
'showmedians' : False,
'points' : 100, # number of points to evaluate for Gaussian KDE
'bw_method' : 'silverman'
}
def_hexbinprops = {
'gridsize' : (50,50),
'mincnt' : 1,
'xscale' : 'linear',
'yscale' : 'linear',
'lw' : axwidth/4.
}
def_contourprops = {
'linewidths' : sizeline/2,
'linestyles' : 'solid'
}
def_vplineprops = {
'lw' : axwidth,
'color' : defcolor
}
def_figprops = {
'transparent' : True,
'bbox_inches' : 'tight'
}
def_tickprops_boxed = {
'length' : ticklength/1.75,
'width' : axwidth/1.75,
'pad' : tickpad,
'axis' : 'both',
'direction' : 'in',
'colors' : textcolor,
'bottom' : True,
'left' : True,
'top' : True,
'right' : True
}
def_minortickprops_boxed = {
'length' : (ticklength/1.75)-1.25,
'width' : axwidth/1.75,
'axis' : 'both',
'direction' : 'in',
'which' : 'minor',
'colors' : textcolor
}
def_axprops_ppt = {
'linewidth' : 2 * axwidth,
'linestyle' : '-',
'color' : textcolor
}
def_tickprops_ppt = {
'length' : ticklength,
'width' : axwidth,
'pad' : tickpad,
'axis' : 'both',
'direction' : 'out',
'colors' : textcolor,
'bottom' : True,
'left' : True,
'top' : False,
'right' : False
}
def_minortickprops_ppt = {
'length' : ticklength-1.25,
'width' : axwidth,
'axis' : 'both',
'direction' : 'out',
'which' : 'minor',
'colors' : textcolor
}
singlevartypes = ['hist', 'kde', 'violin']
############# PLOTTING FUNCTIONS #############
def plot(**pdata):
""" Generic plotting routine. Sets basic options then passes parameters to detailed plotting functions. """
# Sanity checks
ndata = 0
assert 'ax' not in pdata or 'save' not in pdata, 'Attempted to save the figure, but the axis has been supplied manually!'
assert ('x' in pdata or 'y' in pdata), 'No data passed to plot!'
if 'x' in pdata and 'y' in pdata:
ndata = len(np.array(pdata['x']).shape)
assert ndata==len(np.array(pdata['y']).shape), 'x (dimension %d) and y (dimension %d) have mismatched shapes!' % (ndata, len(np.array(pdata['y']).shape))
if ndata==1 and not ('type' in pdata and pdata['type']=='circos') and len(np.array(pdata['x'][0]))==1:
pdata['x'] = [pdata['x']]
pdata['y'] = [pdata['y']]
elif 'x' in pdata and 'y' not in pdata:
ndata = len(np.array(pdata['x']).shape)
assert pdata['type'] in singlevartypes, 'Only one set of values passed, but plot type (%s) requires two sets of values to plot!' % pdata['type']
if ndata==1 and len(np.array(pdata['x'][0]))==1: pdata['x'] = [pdata['x']]
elif 'y' in pdata and 'x' not in pdata:
ndata = len(np.array(pdata['y']).shape)
assert pdata['type'] in singlevartypes, 'Only one set of values passed, but plot type (%s) requires two sets of values to plot!' % pdata['type']
pdata['x'] = [k for k in pdata['y']]
pdata['y'] = []
if ndata==1 and len(np.array(pdata['x'][0]))==1: pdata['x'] = [pdata['x']]
if 'colors' not in pdata: assert len(pdata['x'])<9, 'No colors provided, but the number of elements to be plotted (%d) is >8, maximum number of default colors!' % len(pdata['x'])
# If no axis is passed, create the axis
fig = 0
if 'ax' not in pdata:
if 'aspect' not in pdata and 'dims' not in pdata:
fig = plt.figure(figsize=(aspect * plotwidth, plotwidth))
pdata['ax'] = plt.subplot(111)
elif 'aspect' in pdata:
fig = plt.figure(figsize=(pdata['aspect'] * plotwidth, plotwidth))
pdata['ax'] = plt.subplot(111)
elif 'dims' in pdata:
fig = plt.figure(figsize=(pdata['dims'][0], pdata['dims'][1]))
pdata['ax'] = plt.subplot(111)
# Fill style parameters if not passed in pdata
if 'theme' not in pdata: pdata['theme'] = 'open'
if 'type' not in pdata: pdata['type'] = 'scatter'
if 'ticklabelprops' not in pdata: pdata['ticklabelprops'] = def_ticklabelprops
if 'axprops' not in pdata:
if 'ppt' in pdata and pdata['ppt']: pdata['axprops'] = def_axprops_ppt
else: pdata['axprops'] = def_axprops
if 'tickprops' not in pdata:
if 'ppt' in pdata and pdata['ppt']: pdata['tickprops'] = def_tickprops_ppt
elif pdata['theme']=='boxed': pdata['tickprops'] = def_tickprops_boxed
else: pdata['tickprops'] = def_tickprops
if 'minortickprops' not in pdata:
if 'ppt' in pdata and pdata['ppt']: pdata['minortickprops'] = def_minortickprops_ppt
elif pdata['theme']=='boxed': pdata['minortickprops'] = def_minortickprops_boxed
else: pdata['minortickprops'] = def_minortickprops
if 'labelprops' not in pdata: pdata['labelprops'] = def_labelprops
if 'sublabelprops' not in pdata and 'sublabel' in pdata: pdata['sublabelprops'] = def_sublabelprops
if 'sublabelcoords' not in pdata and 'sublabel' in pdata: pdata['sublabelcoords'] = [sublabelx, sublabely]
if 'figprops' not in pdata and 'save' in pdata: pdata['figprops'] = def_figprops
if 'legendprops' not in pdata and 'legend' in pdata: pdata['legendprops'] = def_legendprops
if 'colors' not in pdata:
if len(pdata['x'])==1: pdata['colors'] = [defplotcolor]
elif len(pdata['x'])==2: pdata['colors'] = [k for k in defpaircolor]
else: pdata['colors'] = [k for k in blues[len(pdata['x'])]]
if 'plotprops' not in pdata:
if pdata['type']=='scatter': pdata['plotprops'] = def_scatterprops
if pdata['type']=='error': pdata['plotprops'] = def_errorprops
if pdata['type']=='line': pdata['plotprops'] = def_lineprops
if pdata['type']=='fill': pdata['plotprops'] = def_fillprops
if pdata['type']=='hist': pdata['plotprops'] = def_histprops
if pdata['type']=='bar': pdata['plotprops'] = def_barprops
if pdata['type']=='kde': pdata['plotprops'] = def_lineprops
if pdata['type']=='circos': pdata['plotprops'] = def_lineprops
if pdata['type']=='violin': pdata['plotprops'] = def_violinprops
if pdata['type']=='hexbin': pdata['plotprops'] = def_hexbinprops
if pdata['type']=='contour': pdata['plotprops'] = def_contourprops
# Fill in x axis limits and ticks if not passed in pdata
if pdata['type']=='circos' and 'xticks' not in pdata: pdata['xticks'] = []
if pdata['type']=='circos' and 'yticks' not in pdata: pdata['yticks'] = []
if 'xlim' not in pdata: pdata['xlim'] = [np.min([np.min(x) for x in pdata['x']]), np.max([np.max(x) for x in pdata['x']])]
if 'xticks' not in pdata:
xtick, xminortick = [], []
if 'logx' in pdata and pdata['logx']: xtick, xminortick = getlogticks(pdata['xlim'])
else: xtick, xminortick = getticks(pdata['xlim'])
pdata['xticks'] = xtick
if 'xminorticks' not in pdata: pdata['xminorticks'] = xminortick
if 'xminorticks' not in pdata: pdata['xminorticks'] = []
if 'bins' not in pdata and pdata['type']=='hist':
width = (pdata['xlim'][1]-pdata['xlim'][0])/nbins
bins = np.arange(pdata['xlim'][0], pdata['xlim'][1]+width, width)
pdata['bins'] = bins
if 'combine' not in pdata and pdata['type']=='hist': pdata['combine'] = False
# Fill in y axis limits and ticks
if 'ylim' not in pdata and pdata['type'] not in singlevartypes:
pdata['ylim'] = [np.min([np.min(y) for y in pdata['y']]), np.max([np.max(y) for y in pdata['y']])]
elif 'ylim' not in pdata:
ymin = 1.0
ymax = 0.0
if pdata['type']=='hist':
for i in range(len(pdata['x'])):
w = np.ones_like(pdata['x'][i])/float(len(pdata['x'][i]))
h, bin_edges = np.histogram(pdata['x'][i], weights=w, range=pdata['xlim'], bins=pdata['bins'])
if np.min(h)<ymin: ymin = np.min(h)
if np.max(h)>ymax: ymax = np.max(h)
elif pdata['type']=='kde':
for i in range(len(pdata['x'])):
ypdf = gaussian_kde(pdata['x'][i], bw_method='silverman')
x = np.linspace(np.min(pdata['xticks']), np.max(pdata['xticks']), 300)
if np.min(ypdf(x))<ymin: ymin = np.min(ypdf(x))
if np.max(ypdf(x))>ymax: ymax = np.max(ypdf(x))
elif pdata['type']=='violin':
ymax = len(pdata['x'])
if 'positions' in pdata:
ymin = np.min(pdata['positions'])
ymax = np.max(pdata['positions'])
pdata['ylim'] = [ymin, ymax]
if 'yticks' not in pdata:
ytick, yminortick = [], []
if 'logy' in pdata and pdata['logy']: ytick, yminortick = getlogticks(pdata['ylim'])
else: ytick, yminortick = getticks(pdata['ylim'])
pdata['yticks'] = ytick
if 'yminorticks' not in pdata: pdata['yminorticks'] = yminortick
if 'yminorticks' not in pdata: pdata['yminorticks'] = []
if pdata['type']=='fill' and 'y2' not in pdata: pdata['y2']=0
# Sanity check for ticks and log scale
if 'logx' in pdata and pdata['logx']:
assert pdata['xlim'][0]>0, 'Attempting to plot x on a log scale, but the lower limit (%lf) is <= 0!' % pdata['xlim'][0]
if 'xticks' not in pdata:
xtick, xminortick = getlogticks(pdata['xlim'])
pdata['xticks'] = xtick
if 'xminorticks' not in pdata: pdata['xminorticks'] = xminortick
else: pdata['logx'] = False
if 'logy' in pdata and pdata['logy'] and pdata['type'] not in singlevartypes:
assert pdata['ylim'][0]>0, 'Attempting to plot y on a log scale, but the lower limit (%lf) is <= 0!' % pdata['ylim'][0]
if 'yticks' not in pdata:
ytick, yminortick = getlogticks(pdata['ylim'])
pdata['yticks'] = ytick
if 'yminorticks' not in pdata: pdata['yminorticks'] = yminortick
else: pdata['logy'] = False
# Make plot
if pdata['type']=='scatter': scatter(**pdata)
elif pdata['type']=='error': error(**pdata)
elif pdata['type']=='line': line(**pdata)
elif pdata['type']=='fill': fill(**pdata)
elif pdata['type']=='hist': hist(**pdata)
elif pdata['type']=='bar': bar(**pdata)
elif pdata['type']=='kde': kde(**pdata)
elif pdata['type']=='circos': circos(**pdata)
elif pdata['type']=='violin': violin(**pdata)
elif pdata['type']=='hexbin': hexbin(**pdata)
elif pdata['type']=='contour': contour(**pdata)
# Set plot appearance and plot axes
if ('orientation' in pdata['plotprops']) and (pdata['plotprops']['orientation']=='horizontal'):
temp = [k for k in pdata['xlim']]
pdata['xlim'] = [k for k in pdata['ylim']]
pdata['ylim'] = [k for k in temp]
temp = [k for k in pdata['xticks']]
pdata['xticks'] = [k for k in pdata['yticks']]
pdata['yticks'] = [k for k in temp]
temp = [k for k in pdata['xminorticks']]
pdata['xminorticks'] = [k for k in pdata['yminorticks']]
pdata['yminorticks'] = [k for k in temp]
if pdata['theme']=='open':
adjustlim(pdata['xlim'], logscale=pdata['logx'])
adjustlim(pdata['ylim'], logscale=pdata['logy'])
if 'nudgex' in pdata: pdata['xlim'][1] *= pdata['nudgex']
if 'nudgey' in pdata: pdata['ylim'][1] *= pdata['nudgey']
setappearance(**pdata)
# Save
if 'save' in pdata:
plt.savefig(pdata['save']+'.pdf', **pdata['figprops'])
plt.close(fig)
def scatter(**pdata):
""" Generic scatter plot. """
# Plot data
hollowprops = pdata['plotprops'].copy()
hollowprops['lw'] = 1
hollowprops['facecolor'] = 'none'
for i in range(len(pdata['x'])):
x = pdata['x'][i]
y = pdata['y'][i]
if 'facecolor' in pdata and pdata['facecolor'][i] and 'edgecolor' in pdata and pdata['edgecolor'][i]:
cf = pdata['facecolor'][i]
ce = pdata['edgecolor'][i]
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].scatter(x, y, edgecolor=ce, **hollowprops)
else: pdata['ax'].scatter(x, y, facecolor=cf, edgecolor=ce, **pdata['plotprops'])
elif 'colors' in pdata and pdata['colors'][i]:
c = pdata['colors'][i]
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].scatter(x, y, edgecolor=c, **hollowprops)
else: pdata['ax'].scatter(x, y, facecolor=c, edgecolor=c, **pdata['plotprops'])
else:
c = defcolor
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].scatter(x, y, edgecolor=c, **hollowprops)
else: pdata['ax'].scatter(x, y, facecolor=c, edgecolor=c, **pdata['plotprops'])
# Make legend (optional)
if 'legend' in pdata:
x = [10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
if 'facecolor' in pdata and pdata['facecolor'][i] and 'edgecolor' in pdata and pdata['edgecolor'][i]:
cf = pdata['facecolor'][i]
ce = pdata['edgecolor'][i]
l = pdata['legend'][i]
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].scatter(x, y, edgecolor=ce, label=l, zorder=len(pdata['x'])-i+10, **hollowprops)
else: pdata['ax'].scatter(x, y, facecolor=cf, edgecolor=ce, label=l, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
else:
c = defcolor
if 'colors' in pdata and pdata['colors'][i]: c = pdata['colors'][i]
l = pdata['legend'][i]
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].scatter(x, y, edgecolor=c, label=l, zorder=len(pdata['x'])-i+10, **hollowprops)
else: pdata['ax'].scatter(x, y, facecolor=c, edgecolor=c, label=l, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
#for text in l.get_texts(): text.set_size(sizelabel)
def error(**pdata):
""" Generic errorbar plot. """
# Plot data
hollowprops = pdata['plotprops'].copy()
hollowprops['mew'] = 1
hollowprops['mfc'] = 'none'
for i in range(len(pdata['x'])):
x = pdata['x'][i]
y = pdata['y'][i]
xerr = None
yerr = None
if 'xerr' in pdata and np.any(pdata['xerr']) and np.any(pdata['xerr'][i]): xerr = pdata['xerr'][i]
if 'yerr' in pdata and np.any(pdata['yerr']) and np.any(pdata['yerr'][i]): yerr = pdata['yerr'][i]
if 'facecolor' in pdata and pdata['facecolor'][i] and 'edgecolor' in pdata and pdata['edgecolor'][i]:
cf = pdata['facecolor'][i]
ce = pdata['edgecolor'][i]
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].errorbar(x, y, xerr=xerr, yerr=yerr, mec=ce, color=ce, zorder=len(pdata['x'])-i+10, **hollowprops)
else: pdata['ax'].errorbar(x, y, xerr=xerr, yerr=yerr, mfc=cf, mec=ce, color=ce, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
elif 'colors' in pdata and pdata['colors'][i]:
c = pdata['colors'][i]
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].errorbar(x, y, xerr=xerr, yerr=yerr, mec=c, color=c, zorder=len(pdata['x'])-i+10, **hollowprops)
else: pdata['ax'].errorbar(x, y, xerr=xerr, yerr=yerr, mfc=c, mec=c, color=c, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
else:
c = defcolor
if 'hollow' in pdata and pdata['hollow'][i]: pdata['ax'].errorbar(x, y, xerr=xerr, yerr=yerr, mec=c, color=c, zorder=len(pdata['x'])-i+10, **hollowprops)
else: pdata['ax'].errorbar(x, y, xerr=xerr, yerr=yerr, mfc=c, mec=c, color=c, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
# for i in range(len(pdata['x'])):
# c = pdata['colors'][i]
# x = pdata['x'][i]
# y = pdata['y'][i]
#
# if 'xerr' in pdata:
# if 'yerr' in pdata: pdata['ax'].errorbar(x, y, xerr=pdata['xerr'][i], yerr=pdata['yerr'][i], c=c, mfc=c, mec=c, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
# else: pdata['ax'].errorbar(x, y, xerr=pdata['xerr'][i], c=c, mfc=c, mec=c, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
# elif 'yerr' in pdata: pdata['ax'].errorbar(x, y, yerr=pdata['yerr'][i], c=c, mfc=c, mec=c, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
# else: pdata['ax'].errorbar(x, y, c=c, mfc=c, mec=c, zorder=len(pdata['x'])-i+10, **pdata['plotprops'])
# Make legend (optional)
if 'legend' in pdata:
x = [10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].scatter(x, y, facecolor=c, edgecolor=c, label=l, **def_scatterprops)
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
def line(**pdata):
""" Generic line plot. """
# Plot data
for i in range(len(pdata['x'])):
c = pdata['colors'][i]
x = pdata['x'][i]
y = pdata['y'][i]
if 'zorder' not in pdata['plotprops']: pdata['ax'].plot(x, y, color=c, zorder=len(pdata['x'])-i, **pdata['plotprops'])
else: pdata['ax'].plot(x, y, color=c, **pdata['plotprops'])
# if 'legend' in pdata:
# pdata['ax'].plot(x, y, color=c, zorder=len(pdata['x'])-i, label=pdata['legend'][i], **pdata['plotprops'])
#
# else:
# pdata['ax'].plot(x, y, color=c, zorder=len(pdata['x'])-i, **pdata['plotprops'])
# Make legend (optional)
if 'legend' in pdata:# and 'plotlegend' in pdata:
x = [10 * pdata['xlim'][1], 10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1], 10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].plot(x, y, color=c, label=l, **pdata['plotprops'])
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
def fill(**pdata):
""" Generic filled line plot. """
# Plot data
for i in range(len(pdata['x'])):
c = pdata['colors'][i]
x = pdata['x'][i]
y = pdata['y'][i]
if 'zorder' not in pdata['plotprops']: pdata['ax'].fill_between(x, y, color=c, zorder=len(pdata['x'])-i, **pdata['plotprops'])
else: pdata['ax'].fill_between(x, y, color=c **pdata['plotprops'])
# Make legend (optional)
if 'legend' in pdata:# and 'plotlegend' in pdata:
x = [10 * pdata['xlim'][1], 10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1], 10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].plot(x, y, color=c, label=l, **pdata['plotprops'])
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
def hist(**pdata):
""" Generic histogram. """
# Plot data
if pdata['combine']: n, bins, patches = pdata['ax'].hist(pdata['x'], weights=[np.ones_like(x)/float(len(x)) for x in pdata['x']], color=pdata['colors'], bins=pdata['bins'], **pdata['plotprops'])
else:
for i in range(len(pdata['x'])):
c = pdata['colors'][i]
x = pdata['x'][i]
w = np.ones_like(x)/float(len(x))
if 'weights' in pdata: w = pdata['weights'][i]
if 'percent' in pdata and pdata['percent']: w *= 100.0
n, bins, patches = pdata['ax'].hist(x, weights=w, facecolor=c, zorder=len(pdata['x'])-i, bins=pdata['bins'], range=(pdata['xlim'][0], pdata['xlim'][1]), **pdata['plotprops'])
for patch in patches: patch.set_facecolor(c)
# Make legend (optional)
if 'legend' in pdata:
x = [10 * pdata['xlim'][1], 10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1], 10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].scatter(x, y, facecolor=c, edgecolor=c, label=l, **def_scatterprops)
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
# Annotate (optional)
if 'annotate' in pdata:
for i in range(len(pdata['annotate'])):
pdata['ax'].text(pdata['annotate'][i][0], pdata['annotate'][i][1], pdata['annotate'][i][2], **pdata['ticklabelprops'])
def bar(**pdata):
""" Generic bar graph. """
# Check alignment
isHorizontal = False
if pdata['plotprops']['orientation'] and pdata['plotprops']['orientation']=='horizontal':
isHorizontal = True
if 'width' in pdata['plotprops']:
pdata['plotprops']['height'] = pdata['plotprops']['width']
del pdata['plotprops']['width']
del pdata['plotprops']['orientation']
else: pdata['plotprops']['orientation'] = 'vertical'
# Plot data
for i in range(len(pdata['x'])):
c = pdata['colors'][i]
x = pdata['x'][i]
y = pdata['y'][i]
xerr = None
yerr = None
err_kw = {}
if 'xerr' in pdata and np.any(pdata['xerr']) and np.any(pdata['xerr'][i]): xerr = pdata['xerr'][i]
if 'yerr' in pdata and np.any(pdata['yerr']) and np.any(pdata['yerr'][i]): yerr = pdata['yerr'][i]
if xerr or yerr: err_kw = { 'ecolor' : defcolor, 'capsize' : 0 }
if isHorizontal: pdata['ax'].barh(x, y, xerr=xerr, yerr=yerr, color=c, zorder=len(pdata['x'])-1-i, error_kw=err_kw, **pdata['plotprops'])
else: pdata['ax'].bar( x, y, xerr=xerr, yerr=yerr, color=c, zorder=len(pdata['x'])-1-i, error_kw=err_kw, **pdata['plotprops'])
# Make legend (optional)
if 'legend' in pdata:
x = [10 * pdata['xlim'][1], 10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1], 10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].scatter(x, y, facecolor=c, edgecolor=c, label=l, **def_scatterprops)
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
# Annotate (optional)
if 'annotate' in pdata:
for i in range(len(pdata['annotate'])):
pdata['ax'].text(pdata['annotate'][i][0], pdata['annotate'][i][1], pdata['annotate'][i][2], **pdata['ticklabelprops'])
if isHorizontal: pdata['plotprops']['orientation'] = 'horizontal'
def kde(**pdata):
""" Generic kde-smoothed plot. """
# Plot data
for i in range(len(pdata['x'])):
c = pdata['colors'][i]
y = pdata['x'][i]
ypdf = gaussian_kde(y, bw_method='silverman')
x = np.linspace(np.min(pdata['xticks']), np.max(pdata['xticks']), 300)
pdata['ax'].plot(x, ypdf(x), color=c, zorder=len(pdata['x'])-i, **pdata['plotprops'])
# Make legend (optional)
if 'legend' in pdata:
x = [10 * pdata['xlim'][1], 10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1], 10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].plot(x, y, color=c, label=l, **pdata['plotprops'])
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
def circos(**pdata):
""" Generic circos-style plot. """
# Generate Bezier curves using index to angle map
if 't' not in pdata:
pdata['t'] = np.arange(0., 1.01, 0.01)
if 'rad' not in pdata:
pdata['rad'] = [[0.8, 0.8] for i in range(len(pdata['x']))]
if 'size' not in pdata:
pdata['size'] = float(np.max([np.max(pdata['x']), np.max(pdata['y'])]))
if 'bezrad' not in pdata:
pdata['bezrad'] = 0.
if not hasattr(pdata['bezrad'], '__len__'):
temp = pdata['bezrad']
pdata['bezrad'] = [temp for i in range(len(pdata['rad']))]
if 'angle' not in pdata:
pdata['angle'] = [[-2 * np.pi * pdata['x'][i] / pdata['size'], -2 * np.pi * pdata['y'][i] / pdata['size']] for i in range(len(pdata['x']))]
cpolar = bezier(pdata['rad'], pdata['angle'], pdata['t'], pdata['bezrad'])
# Plot data
for i in range(len(pdata['x'])):
c = pdata['colors'][i]
x = cpolar[i][0]
y = cpolar[i][1]
if 'arcprops' in pdata: pdata['ax'].plot(x, y, color=c, zorder=len(pdata['x'])-i, **pdata['arcprops'][i])
else: pdata['ax'].plot(x, y, color=c, zorder=len(pdata['x'])-i, **pdata['plotprops'])
# Add labels (optional)
if 'ticklabels' in pdata:
for tl in pdata['ticklabels']:
t = -2 * np.pi * tl[0] / pdata['size']
r = 0.85
l = tl[0]
if len(tl)>1: r = tl[1]
if len(tl)>2: l = tl[2]
if t>-np.pi/2. or t<-3.*np.pi/2.: pdata['ax'].text(r * np.cos(t), r * np.sin(t), l, rotation_mode='anchor', rotation=rad2deg(t), ha='left', va='center', **pdata['ticklabelprops'])
else: pdata['ax'].text(r * np.cos(t), r * np.sin(t), l, rotation_mode='anchor', rotation=rad2deg(t)+180., ha='right', va='center', **pdata['ticklabelprops'])
if 'textlabels' in pdata:
for tl in pdata['textlabels']:
t = -2 * np.pi * tl[0] / pdata['size']
r = tl[1]
l = tl[2]
if t>-np.pi/2. or t<-3.*np.pi/2.: pdata['ax'].text(r * np.cos(t), r * np.sin(t), l, rotation_mode='anchor', rotation=rad2deg(t), ha='left', va='center', **pdata['labelprops'])
else: pdata['ax'].text(r * np.cos(t), r * np.sin(t), l, rotation_mode='anchor', rotation=rad2deg(t)+180., ha='right', va='center', **pdata['labelprops'])
# Make legend (optional)
if 'legend' in pdata:
x = [10 * pdata['xlim'][1], 10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1], 10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].plot(x, y, color=c, label=l, **pdata['plotprops'])
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
#for text in l.get_texts(): text.set_size(sizelabel+1)
def violin(**pdata):
""" Generic violin plot. """
# Plot data
for i in range(len(pdata['x'])):
x = pdata['x'][i]
pos = [i+1]
if 'positions' in pdata: pos = pdata['positions'][i]
#print(pos)
#print(len(x))
#vp = pdata['ax'].violinplot(x, **pdata['plotprops'])
vp = pdata['ax'].violinplot(x, positions=pos, **pdata['plotprops'])
# Adjust appearance
c = defcolor
fc = defcolor
ec = defcolor
if 'colors' in pdata:
c = pdata['colors'][i]
fc = pdata['colors'][i]
ec = pdata['colors'][i]
if 'facecolor' in pdata:
fc = pdata['facecolor'][i]
if 'edgecolor' in pdata:
fc = pdata['edgecolor'][i]
for body in vp['bodies']:
body.set_facecolor(fc)
body.set_edgecolor(ec)
body.set_linewidth(axwidth)
showLines = ['cmins', 'cmaxes', 'cmeans', 'cmedians']
hideLines = ['cbars']
for line in [vp[l] for l in showLines if l in vp]:
line.set_color(c)
line.set_linewidth(axwidth)
for line in [vp[l] for l in hideLines if l in vp]:
line.set_linewidth(0)
# Make legend (optional)
if 'legend' in pdata:
x = [10 * pdata['xlim'][1], 10 * pdata['xlim'][1]]
y = [10 * pdata['ylim'][1], 10 * pdata['ylim'][1]]
for i in range(len(pdata['legend'])):
c = pdata['colors'][i]
l = pdata['legend'][i]
pdata['ax'].plot(x, y, color=c, label=l, **pdata['plotprops'])
l = pdata['ax'].legend(**pdata['legendprops'])
for text in l.get_texts(): text.set_color(textcolor)
def hexbin(**pdata):
""" 2D histogram with hexagonal bins. """
# Plot data
for i in range(len(pdata['x'])):
x = pdata['x'][i]
y = pdata['y'][i]
hb = pdata['ax'].hexbin(x, y, **pdata['plotprops'])
# Annotate (optional)
if 'annotate' in pdata:
for i in range(len(pdata['annotate'])):
pdata['ax'].text(pdata['annotate'][i][0], pdata['annotate'][i][1], pdata['annotate'][i][2], **pdata['ticklabelprops'])
def contour(**pdata):
""" Generic contour plot. """
# Sort out contour shading plot props from line props
cShade = ['cmap', 'hatches']
cLine = ['linewidths', 'linestyles']
# Plot data
for i in range(len(pdata['x'])):
x = pdata['x'][i]
y = pdata['y'][i]
z = pdata['z'][i]
tempprops = deepcopy(pdata['plotprops'])
for prop in cLine:
if prop in tempprops: del tempprops[prop]
if 'colors' in tempprops and 'cmap' in tempprops: del tempprops['colors']
pdata['ax'].contourf(x, y, z, **tempprops)
tempprops = deepcopy(pdata['plotprops'])
for prop in cShade:
if prop in tempprops: del tempprops[prop]
pdata['ax'].contour(x, y, z, **tempprops)
# Annotate (optional)
if 'annotate' in pdata:
for i in range(len(pdata['annotate'])):
pdata['ax'].text(pdata['annotate'][i][0], pdata['annotate'][i][1], pdata['annotate'][i][2], **pdata['ticklabelprops'])
def setappearance(**pdata):
""" Set out general plot appearance (axis labels, tick parameters, etc). """
# Make axis invisible
if 'noaxes' in pdata and pdata['noaxes']:
for axis in ['left', 'right', 'bottom', 'top']: pdata['ax'].spines[axis].set_visible(False)
elif pdata['theme']=='boxed':
for axis in ['left', 'right', 'bottom', 'top']: pdata['ax'].spines[axis].set_visible(True)
elif pdata['theme']=='open':
for axis in ['top', 'right']: pdata['ax'].spines[axis].set_visible(False)
for axis in ['bottom', 'left']: pdata['ax'].spines[axis].set_visible(True)
if 'hide' in pdata:
for axis in pdata['hide']: pdata['ax'].spines[axis].set_visible(False)
if 'show' in pdata:
for axis in pdata['show']: pdata['ax'].spines[axis].set_visible(True)
# Add labels
if 'xlabel' in pdata: pdata['ax'].set_xlabel(pdata['xlabel'], **pdata['labelprops'])
if 'ylabel' in pdata: pdata['ax'].set_ylabel(pdata['ylabel'], **pdata['labelprops'])
if 'sublabel' in pdata: