def set_panel_layout(E, fig, err_type, tbin_type='12bins'):
# legend annotation
if tbin_type.endswith('bins'):
fig.text(.7, 1.1, 'gray background: Dark Cycle', fontsize=8)
xlabel = 'Circadian Time'
add_xylabels(fig, xlabel=xlabel, xypad=-.15, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures vs CT, 12bins group avg$\pm$%s\n%s days: %s' % (
E.short_name, err_type, E.use_days.replace('_',
'-').title(), days_string)
add_titles_notes(E, fig, title=fig_title, typad=.1)
plt.subplots_adjust(hspace=.6, wspace=.6)
def set_panel_layout(E, fig, err_type, tbin_type):
fig.text(.6, .9, '0: %s, control, %s (grayscale)' %(E.strain_names[0], tbin_type), fontsize=8)
fig.text(.6, .85, '1: %s, knock-out, %s (colors)' %(E.strain_names[1], tbin_type), fontsize=8)
if tbin_type.endswith('bins'):
fig.text(.6, .8, 'gray background: Dark Cycle', fontsize=8)
xlabel = 'Circadian Time'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures vs CT, 12bins, group avg$\pm$%s\n%s days: %s' %(
E.short_name, err_type,
E.use_days.replace('_', '-').title(), days_string
)
add_titles_notes(E, fig, title=fig_title)
def plot_features_panel_LC_DC_ratio(experiment,
level='group',
bin_type='3cycles',
err_type='sem',
plot_type='features',
ADD_SOURCE=True):
E = experiment
print "%s, level: %s, bin_type: %s, err_type: %s, days: %s" % (
plot_features_panel_LC_DC_ratio.__name__, level, bin_type, err_type,
E.daysToUse)
features = E.features_by_activity
num_features = len(features)
days_to_use = E.daysToUse
dirname = E.figures_dir + '%s/vectors/panels_expdays/%s/%s_days/' % (
plot_type, bin_type, E.use_days)
if not os.path.isdir(dirname): os.makedirs(dirname)
fname = dirname + '%s_panel_expdays_LC_DC_ratio' % (plot_type
) #s, err_type)
# using mouseday value
# ratios = E.generate_feature_vectors_LC_DC_ratio_expdays(features, level, bin_type, err_type)
# using group averages value
data_ = E.generate_feature_vectors_expdays(features, level, bin_type,
err_type)
ratios_ = data_[:, :, :, 2, 0] / data_[:, :, :, 1, 0] # LC/DC, avgs
figsize = (14.4, 4.8)
nrows, ncols = 4, 7
fig, axes = plt.subplots(nrows, ncols, figsize=figsize, sharex=True)
xs = days_to_use
cnt = 0
for n in xrange(nrows):
for m in xrange(ncols):
ax = axes.flatten()[n * ncols + m]
if n == 0 and m >= 3:
ax.axis('off')
continue
feature = features[cnt]
colors = get_two_group_features_colors(E, feature)
subtitle = '%s %s' % (feature,
E.plot_settings_dict[feature]['unit'])
for g in xrange(E.num_strains):
# # using mouseday values
# tkw = {'fmt':'o-', 'ms':2, 'elinewidth':.5, 'capsize':1}
# ax.errorbar(xs, ratios[g, cnt, :, 0], yerr=ratios[g, cnt, :, 1],
# color=colors[g], mec=colors[g], **tkw)
# using group averages value
tkw = {'marker': 'o', 'ms': 2, 'zorder': 0}
ax.plot(xs,
ratios_[g, cnt, :],
color=colors[g],
mec=colors[g],
**tkw)
# use when plotting all for comparison
# colors_ = ['r', 'y']
# ax.plot(xs, ratios_[g, cnt, :], color=colors_[g], mec=colors_[g], **tkw)
if E.short_name == 'HFD2':
d_day = E.dietChangeDayNumbers[0]
ax.axvspan(xmin=d_day,
xmax=days_to_use[-1],
color='.9',
zorder=0)
xlims = ax.get_xlim()
ax.set_xlim((4, xlims[1]))
ax.set_ylim((0, ax.get_ylim()[1]))
ax_cleanup(ax)
ax.set_title(subtitle, fontsize=10)
cnt += 1
fig.text(.6,
.9,
'0: %s, control, 24H (grayscale)' % E.strain_names[0],
fontsize=8)
fig.text(.6,
.85,
'1: %s, knock-out, 24H (colors)' % E.strain_names[1],
fontsize=8)
fig.text(.6, .8, 'gray background: diet change', fontsize=8)
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures vs days, LC/DC ratio %s avg$\pm$%s\nacross %s days: %s' % (
E.short_name, level, err_type, E.use_days.replace(
'_', '-').title(), days_string)
add_titles_notes(E, fig, title=fig_title)
plt.subplots_adjust(hspace=.6, wspace=.34)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.02)
def plot_features_panel_DC_LC(experiment,
level='group',
bin_type='3cycles',
err_type='sem',
plot_type='features',
ADD_SOURCE=True):
E = experiment
print "%s, level: %s, bin_type: %s, err_type: %s, days: %s" % (
plot_features_panel_DC_LC.__name__, level, bin_type, err_type,
E.daysToUse)
features = E.features_by_activity
num_features = len(features)
days_to_use = E.daysToUse
dirname = E.figures_dir + '%s/vectors/panels_expdays/%s/%s_days/' % (
plot_type, bin_type, E.use_days)
if not os.path.isdir(dirname): os.makedirs(dirname)
fname = dirname + '%s_panel_expdays_DC_LC_group_%s' % (plot_type, err_type)
# groups, features, days, cycles, avg/err
data = E.generate_feature_vectors_expdays(features, level, bin_type,
err_type)
new_data = data[:, :, :, 1:, :]
figsize = (14.4, 4.8)
nrows, ncols = 4, 7
fig, axes = plt.subplots(nrows, ncols, figsize=figsize, sharex=True)
xs = days_to_use
cnt = 0
for n in xrange(nrows):
for m in xrange(ncols):
ax = axes.flatten()[n * ncols + m]
if n == 0 and m >= 3:
ax.axis('off')
continue
feature = features[cnt]
# get colors
if feature.startswith('AS'):
color1, color2 = [E.fcolors['AS'].values()[x] for x in [1, 3]]
elif feature.startswith('T'):
color1, color2 = [
E.fcolors[feature[1:]].values()[x] for x in [1, 3]
]
else:
color1, color2 = [
E.fcolors[feature[:1]].values()[x] for x in [1, 3]
]
colors = ['.4', '.7', color1, color2]
subtitle = '%s %s' % (feature,
E.plot_settings_dict[feature]['unit'])
for g in xrange(E.num_strains):
tkw = {'fmt': 'o-', 'ms': 2, 'elinewidth': .5, 'capsize': 1}
# DC
mec = '0' if g == 0 else colors[2 * g]
ax.errorbar(xs,
new_data[g, cnt, :, 0, 0],
yerr=new_data[g, cnt, :, 0, 1],
color=colors[2 * g],
mec=mec,
**tkw)
#LC
mc = '0' if g == 0 else colors[2 * g + 1]
ax.errorbar(xs,
new_data[g, cnt, :, 1, 0],
yerr=new_data[g, cnt, :, 1, 1],
color=colors[2 * g + 1],
mec=mec,
**tkw)
if E.short_name == 'HFD2':
d_day = E.dietChangeDayNumbers[0]
ax.axvspan(xmin=d_day,
xmax=days_to_use[-1],
color='.9',
zorder=0)
xlims = ax.get_xlim()
ax.set_xlim((4, xlims[1]))
ax.set_ylim([0, ax.get_ylim()[1]])
ax_cleanup(ax)
ax.set_title(subtitle, fontsize=10)
cnt += 1
fig.text(.6,
.9,
'0: %s, control (grayscale)\nDC:black, LC: gray' %
E.strain_names[0],
fontsize=8)
fig.text(.6,
.83,
'1: %s, knock-out (colors)\nDC: dark, LC: light ' %
E.strain_names[1],
fontsize=8)
fig.text(.6, .78, 'gray background: diet change', fontsize=8)
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures, DC vs. LC, %s avg and %s\nacross %s days: %s' % (
E.short_name, level, err_type, E.use_days.replace(
'_', '-').title(), days_string)
add_titles_notes(E, fig, title=fig_title)
plt.subplots_adjust(hspace=.6, wspace=.34)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.02)
def plot_features_panel_12bins(experiment,
level='group',
bin_type='12bins',
err_type='sem',
plot_type='features',
ADD_SOURCE=True):
E = experiment
print "%s, level: %s, bin_type: %s, err_type: %s, days: %s" % (
plot_features_panel_12bins.__name__, level, bin_type, err_type,
E.daysToUse)
features = E.features_by_activity
num_features = len(features)
days_to_use = E.daysToUse
num_bins = int(bin_type.strip('bins'))
tbins = my_utils.get_tbins_string(bin_type)
dirname = E.figures_dir + '%s/vectors/panels_expdays/%s/%s_days/' % (
plot_type, bin_type, E.use_days)
if not os.path.isdir(dirname): os.makedirs(dirname)
data = E.generate_feature_vectors_expdays(features, level, bin_type,
err_type)
ymaxs = get_ymaxs(data)
# stop
for b in xrange(num_bins):
new_data = data[:, :, :, b, :]
figsize = (14.4, 4.8)
nrows, ncols = 4, 7
fig, axes = plt.subplots(nrows, ncols, figsize=figsize, sharex=True)
xs = days_to_use
cnt = 0
for n in xrange(nrows):
for m in xrange(ncols):
ax = axes.flatten()[n * ncols + m]
if n == 0 and m >= 3:
ax.axis('off')
continue
feature = features[cnt]
colors = get_two_group_features_colors(E, feature)
subtitle = '%s %s' % (feature,
E.plot_settings_dict[feature]['unit'])
for g in xrange(E.num_strains):
tkw = {
'fmt': 'o-',
'ms': 2,
'elinewidth': .5,
'capsize': 1
}
ax.errorbar(xs,
new_data[g, cnt, :, 0],
yerr=new_data[g, cnt, :, 1],
color=colors[g],
mec=colors[g],
**tkw)
if E.short_name == 'HFD2':
d_day = E.dietChangeDayNumbers[0]
ax.axvspan(xmin=d_day,
xmax=days_to_use[-1],
color='.9',
zorder=0)
# xmin, xmax = ax.get_xlim()
# ax.set_xlim((xmin-.5, xmax+.5))
# ax.set_ylim([0, ymaxs[cnt]])
ax_cleanup(ax)
ax.set_title(subtitle, fontsize=10)
cnt += 1
xmin, xmax = ax.get_xlim()
ax.set_xlim((xmin - .5, xmax + .5))
fig.text(.6,
.9,
'0: %s, control, %s (grayscale)' %
(E.strain_names[0], tbins[b]),
fontsize=8)
fig.text(.6,
.85,
'1: %s, knock-out, %s (colors)' %
(E.strain_names[1], tbins[b]),
fontsize=8)
fig.text(.6, .8, 'gray background: diet change', fontsize=8)
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel=xlabel, xypad=-.02, labelsize=10)
days_string = E.get_days_to_use_text()
fig_title = '%s Experiment\nFeatures, %s %s avg$\pm$%s, %s\nacross %s days: %s' % (
E.short_name, bin_type, level, err_type, tbins[b],
E.use_days.replace('_', '-').title(), days_string)
add_titles_notes(E, fig, title=fig_title)
plt.subplots_adjust(hspace=.6, wspace=.34)
fname = dirname + '%s_panel_expdays_%s_group_%s_bin%d' % (
plot_type, bin_type, err_type, b)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.02)
def draw_subplot(experiment,
data,
labels,
data_rescaled,
fname,
act='F',
level='mouse',
sub_type='line',
plot_type='ingestion',
ADD_SOURCE=False):
E = experiment
i_act = 0 if act == 'F' else 1
units = ['mg/s', 'g', 'min']
# var_names = [E.HCM_variables[x][i_act] for x in var_types]
varTypes = ['coeffs', 'tots', 'durs']
varNames = [E.HCM_derived['events'][plot_type][x][0] for x in varTypes]
m_labels = np.unique(labels[:, 1])
figsize, nrows, ncols, sharex, sharey = get_subplot_specs(
num_subplots=len(m_labels))
fig, axes = plt.subplots(nrows,
ncols,
figsize=figsize,
sharex=sharex,
sharey=sharey)
colors = [E.fcolors[act].values()[x] for x in [1, 0, 2]]
title, subtitles = get_figure_titles(E,
labels,
act=act,
plot_type=plot_type)
hls = []
for m, mouse in enumerate(m_labels):
try:
ax = axes.flatten()[m]
idx = labels[:, 1] == mouse
arr = data_rescaled[idx]
if sub_type == 'line':
for k, var in enumerate(varNames):
ax.plot(arr[:, k], lw=.5, color=colors[k], label=var)
# ax.axhline(y=arr.mean()[k], c='grey', alpha='.5', label='')
# stop
make_annotation(ax, arr, data, k, idx, colors, units)
elif sub_type == 'bar':
pass
# bar_width = .2
# for k, var in enumerate(varNames):
# ind = np.arange(len(arr)) + k * bar_width -.1
# tkw = {'lw':.2, 'label':var,
# 'color':colors[k], 'edgecolor':None,
# }
# ax.bar(ind, arr[:, k], bar_width, **tkw)
set_layout(E, ax)
ax.set_title(subtitles[m], fontsize=10)
if m == 0:
h, l = ax.get_legend_handles_labels()
except IndexError:
ax.axis('off')
continue
# legend
tkw = {
'ncol': 3,
'fontsize': 8,
'bbox_to_anchor': [0.85, .08],
'frameon': False
}
legend = fig.legend(h, l, **tkw)
for label in legend.get_lines():
label.set_linewidth(3) # the legend line width
# set subplot labels
xlabel = 'Experiment Day'
ylabel = '%s Coefficient' % act
add_xylabels(fig, xlabel, ylabel) #, xypad=0, yxpad=0, labelsize=10)
add_titles_notes(
E,
fig,
title=title,
# typad=typad,
# tlxpad=tlxpad,
# tlypad=typad
)
plt.subplots_adjust(bottom=.12, hspace=0.6, wspace=0.4)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE) #, sypad=-.05)
def draw_histogram_plot(E, mouse_data, arr_preFast, arr_postFast, mouseNumbers,
fname, plot_type, ADD_SOURCE):
# ZeroLight is one group only
# for m in xrange(num_mice):
# data = mouse_data[m]
# label = mouseNumbers[m]
# data_pre, data_post = arr_preFast[m], arr_postFast[m]
# stop
# i_act = 0 if act == 'F' else 1
units = ['mg/s', 'g', 'min']
# var_names = [E.HCM_variables[x][i_act] for x in var_types]
varTypes = ['coeffs', 'tots', 'durs']
varNames = [E.HCM_derived['events'][plot_type][x][0] for x in varTypes]
num_mice = len(mouseNumbers)
figsize = (12.8, 3.6)
nrows, ncols = len(varNames), num_mice
fig, axes = plt.subplots(nrows,
ncols,
figsize=figsize,
sharex=True,
sharey=False)
colors = [E.fcolors['F'].values()[x] for x in [1, 0, 2]]
# title, subtitles = get_figure_titles(E, labels, act=act, plot_type=plot_type)
hls = []
cnt = 0
for m in xrange(nrows): # FC, FT, FD
data = mouse_data[:, :, m]
pre, post = arr_preFast[:, m], arr_postFast[:, m]
for n in xrange(ncols): # mouseNumbers
ax = axes.flatten()[cnt]
# plot quantity across days for each mouse
ax.plot(data[n, :], lw=.5, color=colors[m])
if m == 0:
xmin, xmax = ax.get_xlim()
ax.axhline(xmin=xmin,
xmax=xmax,
y=data[n].mean(0),
linestyle='-',
color=colors[m],
zorder=0,
label='average FC - up to day 35 value')
ax.axhline(xmin=xmin,
xmax=xmax,
y=pre[n],
linestyle='--',
color='g',
zorder=1,
label='day%d, FC 4h-preFast value' %
E.fastDayNumbers[0])
ax.axhline(xmin=xmin,
xmax=xmax,
y=post[n],
linestyle=':',
color='r',
zorder=2,
label='day%d FC 1h-postFast value' %
E.fastDayNumbers[0])
ax.set_title('M%d' % mouseNumbers[n], fontsize=10)
if n == 0:
h, l = ax.get_legend_handles_labels()
if n == 0:
ax.set_ylabel('%s [%s]' % (varNames[m], units[m]), fontsize=10)
ax.set_ylim([.9 * data.min(), 1.1 * data.max()])
set_layout2(E, ax, m, n)
cnt += 1
# legend
tkw = {'fontsize': 8, 'bbox_to_anchor': [0.8, .15], 'frameon': False}
legend = fig.legend(h, l, **tkw)
for label in legend.get_lines():
label.set_linewidth(3) # the legend line width
# set subplot labels
xlabel = 'Experiment Day'
add_xylabels(fig, xlabel)
add_titles_notes(
E,
fig,
title='F-Coefficient, F-Total Amounts, F-Total PhotoBeam BreakTime')
plt.subplots_adjust(bottom=.12) #, hspace=0.6, wspace=0.4)
save_plot(fname, fig, ADD_SOURCE=ADD_SOURCE, sypad=-.03)