def main():
expts = lab.ExperimentSet(
os.path.join(df.metadata_path, 'expt_metadata.xml'),
behaviorDataPath=os.path.join(df.data_path, 'behavior'),
dataPath=os.path.join(df.data_path, 'imaging'))
sal_grp = lab.classes.HiddenRewardExperimentGroup.from_json(
sal_json, expts, label='saline to muscimol')
mus_grp = lab.classes.HiddenRewardExperimentGroup.from_json(
mus_json, expts, label='muscimol to saline')
fig = plt.figure(figsize=(8.5, 11))
gs = plt.GridSpec(1, 1, top=0.9, bottom=0.7, left=0.1, right=0.4)
ax = fig.add_subplot(gs[0, 0])
for expt in mus_grp:
if 'saline' in expt.get('drug'):
expt.attrib['drug_condition'] = 'reversal'
elif 'muscimol' in expt.get('drug'):
expt.attrib['drug_condition'] = 'learning'
for expt in sal_grp:
if 'saline' in expt.get('drug'):
expt.attrib['drug_condition'] = 'learning'
elif 'muscimol' in expt.get('drug'):
expt.attrib['drug_condition'] = 'reversal'
plotting.plot_metric(
ax, [sal_grp, mus_grp], metric_fn=ra.fraction_licks_in_reward_zone,
label_groupby=False, plotby=['X_drug_condition'],
plot_method='swarm', rotate_labels=False,
activity_label='Fraction of licks in reward zone',
colors=sns.color_palette('deep'), plot_bar=True)
ax.set_yticks([0, 0.1, 0.2, 0.3, 0.4])
ax.set_ylim(top=0.4)
ax.set_xticklabels(['Days 1-3', 'Day 4'])
sns.despine(fig)
ax.set_title('')
ax.set_xlabel('')
misc.save_figure(
fig, filename, save_dir=save_dir)
plt.close('all')
def main():
all_grps = df.loadExptGrps('GOL')
WT_expt_grp = all_grps['WT_place_set']
Df_expt_grp = all_grps['Df_place_set']
expt_grps = [WT_expt_grp, Df_expt_grp]
if MALES_ONLY:
for expt_grp in expt_grps:
expt_grp.filter(lambda expt: expt.parent.get('sex') == 'M')
WT_label = WT_expt_grp.label()
Df_label = Df_expt_grp.label()
fig = plt.figure(figsize=(8.5, 11))
gs1 = plt.GridSpec(2,
5,
left=0.1,
right=0.3,
top=0.90,
bottom=0.67,
hspace=0.2)
gs1_2 = plt.GridSpec(2,
5,
left=0.3,
right=0.5,
top=0.90,
bottom=0.67,
hspace=0.2)
WT_1_heatmap_ax = fig.add_subplot(gs1[0, :-1])
WT_3_heatmap_ax = fig.add_subplot(gs1_2[0, :-1])
Df_1_heatmap_ax = fig.add_subplot(gs1[1, :-1])
Df_3_heatmap_ax = fig.add_subplot(gs1_2[1, :-1])
gs_cbar = plt.GridSpec(2,
10,
left=0.3,
right=0.5,
top=0.90,
bottom=0.67,
hspace=0.2)
WT_colorbar_ax = fig.add_subplot(gs_cbar[0, -1])
Df_colorbar_ax = fig.add_subplot(gs_cbar[1, -1])
gs2 = plt.GridSpec(1, 10, left=0.1, right=0.5, top=0.6, bottom=0.45)
pf_close_fraction_ax = fig.add_subplot(gs2[0, :4])
pf_close_behav_corr_ax = fig.add_subplot(gs2[0, 5:])
frac_near_range_2 = (-0.051, 0.551)
behav_range_2 = (-0.051, 0.551)
#
# Heatmaps
#
WT_cmap = sns.light_palette(WT_color, as_cmap=True)
WT_dataframe = lab.ExperimentGroup.dataframe(
WT_expt_grp, include_columns=['X_condition', 'X_day', 'X_session'])
WT_1_expt_grp = WT_expt_grp.subGroup(
list(WT_dataframe[(WT_dataframe['X_condition'] == 'C')
& (WT_dataframe['X_day'] == '0') &
(WT_dataframe['X_session'] == '0')]['expt']))
place.plotPositionHeatmap(WT_1_expt_grp,
roi_filter=WT_filter,
ax=WT_1_heatmap_ax,
norm='individual',
cbar_visible=False,
cmap=WT_cmap,
plotting_order='place_cells_only',
show_belt=False,
reward_in_middle=True)
fix_heatmap_ax(WT_1_heatmap_ax, WT_1_expt_grp)
WT_1_heatmap_ax.set_title(r'Condition $\mathrm{III}$: Day 1')
WT_1_heatmap_ax.set_ylabel(WT_label)
WT_1_heatmap_ax.set_xlabel('')
WT_3_expt_grp = WT_expt_grp.subGroup(
list(WT_dataframe[(WT_dataframe['X_condition'] == 'C')
& (WT_dataframe['X_day'] == '2') &
(WT_dataframe['X_session'] == '0')]['expt']))
place.plotPositionHeatmap(WT_3_expt_grp,
roi_filter=WT_filter,
ax=WT_3_heatmap_ax,
norm='individual',
cbar_visible=True,
cax=WT_colorbar_ax,
cmap=WT_cmap,
plotting_order='place_cells_only',
show_belt=False,
reward_in_middle=True)
fix_heatmap_ax(WT_3_heatmap_ax, WT_3_expt_grp)
WT_3_heatmap_ax.set_title(r'Condition $\mathrm{III}$: Day 3')
WT_3_heatmap_ax.set_ylabel('')
WT_3_heatmap_ax.set_xlabel('')
WT_colorbar_ax.set_yticklabels(['Min', 'Max'])
Df_cmap = sns.light_palette(Df_color, as_cmap=True)
Df_dataframe = lab.ExperimentGroup.dataframe(
Df_expt_grp, include_columns=['X_condition', 'X_day', 'X_session'])
Df_1_expt_grp = Df_expt_grp.subGroup(
list(Df_dataframe[(Df_dataframe['X_condition'] == 'C')
& (Df_dataframe['X_day'] == '0') &
(Df_dataframe['X_session'] == '2')]['expt']))
place.plotPositionHeatmap(Df_1_expt_grp,
roi_filter=Df_filter,
ax=Df_1_heatmap_ax,
norm='individual',
cbar_visible=False,
cmap=Df_cmap,
plotting_order='place_cells_only',
show_belt=False,
reward_in_middle=True)
fix_heatmap_ax(Df_1_heatmap_ax, Df_1_expt_grp)
Df_1_heatmap_ax.set_ylabel(Df_label)
Df_3_expt_grp = Df_expt_grp.subGroup(
list(Df_dataframe[(Df_dataframe['X_condition'] == 'C')
& (Df_dataframe['X_day'] == '2') &
(Df_dataframe['X_session'] == '0')]['expt']))
place.plotPositionHeatmap(Df_3_expt_grp,
roi_filter=Df_filter,
ax=Df_3_heatmap_ax,
norm='individual',
cbar_visible=True,
cax=Df_colorbar_ax,
cmap=Df_cmap,
plotting_order='place_cells_only',
show_belt=False,
reward_in_middle=True)
fix_heatmap_ax(Df_3_heatmap_ax, Df_3_expt_grp)
Df_3_heatmap_ax.set_ylabel('')
Df_colorbar_ax.set_yticklabels(['Min', 'Max'])
#
# Fraction of PCs near reward
#
activity_metric = place.centroid_to_position_threshold
activity_kwargs = {
'method': 'resultant_vector',
'positions': 'reward',
'pcs_only': True,
'threshold': np.pi / 8
}
behavior_fn = ra.fraction_licks_in_reward_zone
behavior_kwargs = {}
behavior_label = 'Fraction of licks in reward zone'
plotting.plot_metric(pf_close_fraction_ax,
expt_grps,
metric_fn=activity_metric,
roi_filters=roi_filters,
groupby=[['expt', 'X_condition', 'X_day']],
plotby=['X_condition', 'X_day'],
plot_abs=False,
plot_method='line',
activity_kwargs=activity_kwargs,
rotate_labels=False,
activity_label='Fraction of place cells near reward',
label_every_n=1,
colors=colors,
markers=markers,
markersize=5,
return_full_dataframes=False,
linestyles=linestyles)
pf_close_fraction_ax.axhline(1 / 8., linestyle='--', color='k')
pf_close_fraction_ax.set_title('')
sns.despine(ax=pf_close_fraction_ax)
pf_close_fraction_ax.set_xlabel('Day in Condition')
day_number_only_label(pf_close_fraction_ax)
label_conditions(pf_close_fraction_ax)
pf_close_fraction_ax.legend(loc='upper left', fontsize=6)
pf_close_fraction_ax.set_ylim(0, 0.40)
pf_close_fraction_ax.set_yticks([0, 0.1, 0.2, 0.3, 0.4])
scatter_kws = {'s': 5}
colorby_list = [(expt_grp.label(), 'C') for expt_grp in expt_grps]
pf_close_behav_corr_ax.set_xlim(frac_near_range_2)
pf_close_behav_corr_ax.set_ylim(behav_range_2)
plotting.plot_paired_metrics(
expt_grps,
first_metric_fn=place.centroid_to_position_threshold,
second_metric_fn=behavior_fn,
roi_filters=roi_filters,
groupby=(('expt', ), ),
colorby=('expt_grp', 'X_condition'),
filter_fn=lambda df: df['X_condition'] == 'C',
filter_columns=['X_condition'],
first_metric_kwargs=activity_kwargs,
second_metric_kwargs=behavior_kwargs,
first_metric_label='Fraction of place cells near reward',
second_metric_label=behavior_label,
shuffle_colors=False,
fit_reg=True,
plot_method='regplot',
colorby_list=colorby_list,
colors=colors,
markers=markers,
ax=pf_close_behav_corr_ax,
scatter_kws=scatter_kws,
truncate=False,
linestyles=linestyles)
pf_close_behav_corr_ax.set_xlim(frac_near_range_2)
pf_close_behav_corr_ax.set_ylim(behav_range_2)
pf_close_behav_corr_ax.tick_params(direction='in')
pf_close_behav_corr_ax.get_legend().set_visible(False)
pf_close_behav_corr_ax.legend(loc='upper left', fontsize=6)
misc.save_figure(fig, filename, save_dir=save_dir)
plt.close('all')
def main():
all_grps = df.loadExptGrps('GOL')
WT_expt_grp = all_grps['WT_hidden_behavior_set']
Df_expt_grp = all_grps['Df_hidden_behavior_set']
behavior_fn = ra.fraction_licks_in_reward_zone
behavior_kwargs = {}
activity_label = 'Fraction of licks in reward zone'
WT_colors = sns.light_palette(WT_color, 8)[::-1]
Df_colors = sns.light_palette(Df_color, 7)[::-1]
markers = ('o', 'v', '^', 'D', '*', 's')
fig, axs = plt.subplots(4, 2, figsize=(8.5, 11))
sns.despine(fig)
wt_ax = axs[0, 0]
df_ax = axs[0, 1]
for ax in list(axs.flat)[2:]:
ax.set_visible(False)
wt_expt_grps = [
WT_expt_grp.subGroup(list(expts['expt']), label=mouse)
for mouse, expts in WT_expt_grp.dataframe(
WT_expt_grp, include_columns=['mouseID']).groupby('mouseID')
]
df_expt_grps = [
Df_expt_grp.subGroup(list(expts['expt']), label=mouse)
for mouse, expts in Df_expt_grp.dataframe(
Df_expt_grp, include_columns=['mouseID']).groupby('mouseID')
]
plotting.plot_metric(wt_ax,
wt_expt_grps,
metric_fn=behavior_fn,
activity_kwargs=behavior_kwargs,
groupby=[['expt'], ['condition_day']],
plotby=['condition_day'],
plot_method='line',
ms=5,
activity_label=activity_label,
colors=WT_colors,
markers=markers,
label_every_n=1,
label_groupby=False,
rotate_labels=False)
wt_ax.set_xlabel('Day in Condition')
wt_ax.set_title(WT_expt_grp.label())
wt_ax.set_yticks([0, 0.1, 0.2, 0.3, 0.4, 0.5])
wt_ax.set_xticklabels(['1', '2', '3', '1', '2', '3', '1', '2', '3'])
label_conditions(wt_ax)
wt_ax.get_legend().set_visible(False)
wt_ax.tick_params(length=3, pad=2)
plotting.plot_metric(df_ax,
df_expt_grps,
metric_fn=behavior_fn,
activity_kwargs=behavior_kwargs,
groupby=[['expt'], ['condition_day']],
plotby=['condition_day'],
plot_method='line',
ms=5,
activity_label=activity_label,
colors=Df_colors,
markers=markers,
label_every_n=1,
label_groupby=False,
rotate_labels=False)
df_ax.set_xlabel('Day in Condition')
df_ax.set_title(Df_expt_grp.label())
df_ax.set_yticks([0, 0.1, 0.2, 0.3, 0.4, 0.5])
df_ax.set_xticklabels(['1', '2', '3', '1', '2', '3', '1', '2', '3'])
label_conditions(df_ax)
df_ax.get_legend().set_visible(False)
df_ax.tick_params(length=3, pad=2)
misc.save_figure(fig, filename, save_dir=save_dir)
def main():
all_grps = df.loadExptGrps('GOL')
WT_expt_grp = all_grps['WT_place_set']
Df_expt_grp = all_grps['Df_place_set']
expt_grps = [WT_expt_grp, Df_expt_grp]
if MALES_ONLY:
for expt_grp in expt_grps:
expt_grp.filter(lambda expt: expt.parent.get('sex') == 'M')
fig = plt.figure(figsize=(8.5, 11))
recur_cdf_ax = fig.add_axes([0.1, 0.70, 0.22, 0.20])
recur_inset_ax = fig.add_axes([0.26, 0.72, 0.05, 0.08])
recur_day_sess_comp_ax = fig.add_axes([0.41, 0.70, 0.15, 0.20])
recur_behav_corr_ax = fig.add_axes([0.65, 0.70, 0.27, 0.20])
stability_over_time_ax = fig.add_axes([0.1, 0.40, 0.22, 0.20])
stability_inset_ax = fig.add_axes([0.26, 0.42, 0.05, 0.08])
stab_day_sess_comp_ax = fig.add_axes([0.41, 0.40, 0.15, 0.20])
stability_behav_corr_ax = fig.add_axes([0.65, 0.40, 0.27, 0.20])
params = {}
params['recur_range'] = (-0.05, 0.85)
params['recur_xticks'] = [0.0, 0.2, 0.4, 0.6, 0.8]
fraction_in_params = {}
fraction_in_params['behavior_fn'] = ra.fraction_licks_in_reward_zone
fraction_in_params['behavior_kwargs'] = {}
fraction_in_params['behavior_label'] = 'Fraction of licks in reward zone'
fraction_in_params['behav_range'] = (-0.05, 0.65)
anticipatory_licking_params = {}
anticipatory_licking_params['behavior_fn'] = ra.fraction_licks_near_rewards
anticipatory_licking_params['behavior_kwargs'] = {
'pre_window_cm': 5,
'exclude_reward': True
}
anticipatory_licking_params['behavior_label'] = \
'Anticipatory licking fraction'
anticipatory_licking_params['behav_range'] = (-0.05, 0.95)
activity_centroid_params = {}
activity_centroid_params['stability_fn'] = place.activity_centroid_shift
activity_centroid_params['stability_kwargs'] = {
'activity_filter': 'active_both',
'circ_var_pcs': circ_var_pcs,
'units': 'rad'
}
activity_centroid_params['stability_label'] = \
'Centroid shift (fraction of belt)'
activity_centroid_params['stab_range'] = (0.90, 2)
act_cent_norm_params = {}
act_cent_norm_params['stability_kwargs'] = {
'activity_filter': 'active_both',
'circ_var_pcs': circ_var_pcs,
'units': 'norm'
}
act_cent_norm_params['stab_range'] = (0.15, 0.31)
act_cent_norm_params['stab_xticks'] = (0.15, 0.20, 0.25, 0.30)
act_cent_norm_params['stab_day_ses_ylim'] = (0.10, 0.3)
act_cent_norm_params['stab_day_ses_yticks'] = (0.1, 0.15, 0.20, 0.25, 0.30)
act_cent_norm_params['stab_inset_ylim'] = (0.15, 0.3)
act_cent_norm_params['stab_inset_yticks'] = (0.15, 0.3)
act_cent_pc_parms = {}
act_cent_pc_parms['stability_kwargs'] = {
'activity_filter': 'pc_both',
'circ_var_pcs': circ_var_pcs,
'units': 'rad'
}
act_cent_cm_params = {}
act_cent_cm_params['stability_kwargs'] = {
'activity_filter': 'active_both',
'circ_var_pcs': circ_var_pcs,
'units': 'cm'
}
act_cent_cm_params['stability_label'] = 'Centroid shift (cm)'
act_cent_cm_params['stab_range'] = (25, 65)
act_cent_cm_params['stab_inset_ylim'] = (0, 50)
act_cent_cm_params['stab_inset_yticks'] = (0, 50)
act_cent_cm_params['stab_day_ses_ylim'] = (30, 50)
pf_corr_params = {}
pf_corr_params['stability_fn'] = place.place_field_correlation
pf_corr_params['stability_kwargs'] = {'activity_filter': 'pc_either'}
pf_corr_params['stability_label'] = 'Place field correlation'
pf_corr_params['stab_range'] = (-0.1, 0.5)
pf_corr_params['stab_xticks'] = (-0.1, 0, 0.1, 0.2, 0.3, 0.4, 0.5)
pf_corr_params['stab_inset_ylim'] = (0, 0.30)
pf_corr_params['stab_inset_yticks'] = (0, 0.30)
pf_corr_params['stab_day_ses_ylim'] = (0, 0.7)
pf_corr_params['stab_day_ses_yticks'] = (0, 0.2, 0.4, 0.6)
pop_vec_corr_params = {}
pop_vec_corr_params['stability_fn'] = place.population_vector_correlation
pop_vec_corr_params['stability_kwargs'] = {
'method': 'corr',
'activity_filter': 'pc_both',
'min_pf_density': 0.05
}
pop_vec_corr_params['stability_label'] = 'Population vector correlation'
#
# Select parameters
#
params.update(fraction_in_params)
params.update(activity_centroid_params)
params.update(act_cent_norm_params)
# params.update(pf_corr_params) # For Supplemental Figure 5
#
# Recurrence
#
day_paired_grps = [
grp.pair('same group',
groupby=['X_session']).pair('consecutive groups',
groupby=['X_condition', 'X_day'])
for grp in expt_grps
]
session_paired_grps = [
grp.pair('consecutive groups',
groupby=['X_condition', 'X_day', 'X_session'])
for grp in expt_grps
]
plotting.plot_metric(recur_cdf_ax,
day_paired_grps,
metric_fn=place.recurrence_probability,
groupby=(('second_expt', ), ),
plot_method='cdf',
roi_filters=roi_filters,
activity_kwargs={'circ_var_pcs': circ_var_pcs},
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label='Recurrence probability',
colors=colors,
rotate_labels=False,
return_full_dataframes=False)
recur_cdf_ax.legend(loc='upper left', fontsize=6)
recur_cdf_ax.set_title('')
recur_cdf_ax.set_xlim(params['recur_range'])
recur_cdf_ax.set_xticks(params['recur_xticks'])
plotting.plot_metric(recur_inset_ax,
day_paired_grps,
metric_fn=place.recurrence_probability,
groupby=(('second_expt', 'second_mouseID'),
('second_mouseID', )),
plot_method='swarm',
roi_filters=roi_filters,
activity_kwargs={'circ_var_pcs': circ_var_pcs},
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label='Recurrence probability',
colors=colors,
rotate_labels=False,
plot_shuffle_as_hline=True,
linewidth=0.2,
edgecolor='gray')
recur_inset_ax.get_legend().set_visible(False)
sns.despine(ax=recur_inset_ax)
recur_inset_ax.set_title('')
recur_inset_ax.set_ylabel('')
recur_inset_ax.set_xlabel('')
recur_inset_ax.tick_params(bottom=False, labelbottom=False)
recur_inset_ax.set_ylim(0, 1.)
recur_inset_ax.set_yticks([0, 1.])
#
# Recurrence - behavior correlation
#
scatter_kws = {'s': 5}
colorby_list = [(expt_grp.label(), ) for expt_grp in expt_grps]
recur_behav_corr_ax.set_xlim(params['recur_range'])
recur_behav_corr_ax.set_ylim(params['behav_range'])
plotting.plot_paired_metrics(
day_paired_grps,
first_metric_fn=place.recurrence_probability,
second_metric_fn=params['behavior_fn'],
roi_filters=roi_filters,
groupby=(('second_expt', ), ),
colorby=['expt_grp'],
filter_fn=None,
filter_columns=None,
first_metric_kwargs=None,
second_metric_kwargs=params['behavior_kwargs'],
first_metric_label='Recurrence probability',
second_metric_label=params['behavior_label'],
shuffle_colors=False,
fit_reg=True,
plot_method='regplot',
colorby_list=colorby_list,
colors=colors,
markers=markers,
ax=recur_behav_corr_ax,
scatter_kws=scatter_kws,
truncate=False,
linestyles=linestyles)
recur_behav_corr_ax.set_xlim(params['recur_range'])
recur_behav_corr_ax.set_ylim(params['behav_range'])
recur_behav_corr_ax.tick_params(direction='in')
recur_behav_corr_ax.legend(loc='upper left', fontsize=6)
#
# Stability
#
filter_fn = None
filter_columns = None
plotting.plot_metric(stability_over_time_ax,
day_paired_grps,
metric_fn=params['stability_fn'],
groupby=(('second_expt', ), ),
plotby=None,
plot_method='cdf',
roi_filters=roi_filters,
activity_kwargs=params['stability_kwargs'],
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label=params['stability_label'],
colors=colors,
rotate_labels=False,
filter_fn=filter_fn,
filter_columns=filter_columns,
return_full_dataframes=False)
stability_over_time_ax.legend(loc='upper left', fontsize=6)
stability_over_time_ax.set_title('')
stability_over_time_ax.set_xlabel(params['stability_label'])
stability_over_time_ax.set_xlim(params['stab_range'])
stability_over_time_ax.set_xticks(params['stab_xticks'])
plotting.plot_metric(stability_inset_ax,
day_paired_grps,
metric_fn=params['stability_fn'],
groupby=(
('second_expt', 'second_mouseID'),
('second_mouseID', ),
),
plotby=None,
plot_method='swarm',
roi_filters=roi_filters,
activity_kwargs=params['stability_kwargs'],
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label=params['stability_label'],
colors=colors,
rotate_labels=False,
filter_fn=filter_fn,
filter_columns=filter_columns,
plot_shuffle_as_hline=True,
linewidth=0.2,
edgecolor='gray')
stability_inset_ax.get_legend().set_visible(False)
sns.despine(ax=stability_inset_ax)
stability_inset_ax.set_title('')
stability_inset_ax.set_ylabel('')
stability_inset_ax.set_xlabel('')
stability_inset_ax.tick_params(bottom=False, labelbottom=False)
stability_inset_ax.set_ylim(params['stab_inset_ylim'])
stability_inset_ax.set_yticks(params['stab_inset_yticks'])
#
# Stability - behavior correlation
#
scatter_kws = {'s': 5}
colorby_list = [(expt_grp.label(), ) for expt_grp in expt_grps]
stability_behav_corr_ax.set_xlim(params['stab_range'])
stability_behav_corr_ax.set_ylim(params['behav_range'])
plotting.plot_paired_metrics(
day_paired_grps,
first_metric_fn=params['stability_fn'],
second_metric_fn=params['behavior_fn'],
roi_filters=roi_filters,
groupby=(('second_expt', ), ),
colorby=['expt_grp'],
filter_fn=filter_fn,
filter_columns=filter_columns,
first_metric_kwargs=params['stability_kwargs'],
second_metric_kwargs=params['behavior_kwargs'],
first_metric_label=params['stability_label'],
second_metric_label=params['behavior_label'],
shuffle_colors=False,
fit_reg=True,
plot_method='regplot',
colorby_list=colorby_list,
colors=colors,
markers=markers,
ax=stability_behav_corr_ax,
scatter_kws=scatter_kws,
truncate=False,
linestyles=linestyles)
stability_behav_corr_ax.tick_params(direction='in')
stability_behav_corr_ax.set_xlim(params['stab_range'])
stability_behav_corr_ax.set_ylim(params['behav_range'])
stability_behav_corr_ax.set_xticks(params['stab_xticks'])
stability_behav_corr_ax.set_xlabel(params['stability_label'])
stability_behav_corr_ax.legend(loc='upper right', fontsize=6)
#
# Day vs. session elapsed comparison
#
filter_fn = None
filter_columns = None
line_kwargs = {'markersize': 4}
plotting.plot_metric(recur_day_sess_comp_ax,
session_paired_grps,
metric_fn=place.recurrence_probability,
groupby=(('elapsed_days_int', 'second_expt',
'second_mouseID'), ),
plotby=('elapsed_days_int', ),
plot_method='box_and_line',
roi_filters=roi_filters,
markers=markers,
activity_kwargs={'circ_var_pcs': circ_var_pcs},
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label='Recurrence probability',
colors=colors,
rotate_labels=False,
plot_shuffle_as_hline=True,
flierprops={
'markersize': 2,
'marker': 'o'
},
box_width=0.4,
box_spacing=0.2,
return_full_dataframes=False,
whis='range',
linestyles=linestyles,
notch=False,
line_kwargs=line_kwargs)
sns.despine(ax=recur_day_sess_comp_ax)
recur_day_sess_comp_ax.legend(loc='upper right', fontsize=6)
recur_day_sess_comp_ax.set_title('')
recur_day_sess_comp_ax.set_xlabel('')
recur_day_sess_comp_ax.set_xticklabels(['S-S', 'D-D'])
recur_day_sess_comp_ax.set_ylim(0.0, 1.0)
recur_day_sess_comp_ax.set_yticks([0.00, 0.25, 0.50, 0.75, 1.])
plotting.plot_metric(stab_day_sess_comp_ax,
session_paired_grps,
metric_fn=params['stability_fn'],
groupby=(('elapsed_days_int', 'second_expt',
'second_mouseID'), ),
plotby=('elapsed_days_int', ),
plot_method='box_and_line',
roi_filters=roi_filters,
activity_kwargs=params['stability_kwargs'],
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label=params['stability_label'],
colors=colors,
rotate_labels=False,
filter_fn=filter_fn,
markers=markers,
filter_columns=filter_columns,
plot_shuffle_as_hline=True,
flierprops={
'markersize': 2,
'marker': 'o'
},
box_width=0.4,
box_spacing=0.2,
return_full_dataframes=False,
whis='range',
linestyles=linestyles,
notch=False,
line_kwargs=line_kwargs)
sns.despine(ax=stab_day_sess_comp_ax)
stab_day_sess_comp_ax.legend(loc='upper right', fontsize=6)
stab_day_sess_comp_ax.set_title('')
stab_day_sess_comp_ax.set_xlabel('')
stab_day_sess_comp_ax.set_ylabel(params['stability_label'])
stab_day_sess_comp_ax.set_xticklabels(['S-S', 'D-D'])
stab_day_sess_comp_ax.set_ylim(params['stab_day_ses_ylim'])
stab_day_sess_comp_ax.set_yticks(params['stab_day_ses_yticks'])
misc.save_figure(fig, filename, save_dir=save_dir)
plt.close('all')
def main():
hidden_grps = df.loadExptGrps('GOL')
WT_expt_grp_hidden = hidden_grps['WT_place_set']
Df_expt_grp_hidden = hidden_grps['Df_place_set']
expt_grps_hidden = [WT_expt_grp_hidden, Df_expt_grp_hidden]
acute_grps = df.loadExptGrps('RF')
WT_expt_grp_acute = acute_grps['WT_place_set'].unpair()
Df_expt_grp_acute = acute_grps['Df_place_set'].unpair()
expt_grps_acute = [WT_expt_grp_acute, Df_expt_grp_acute]
WT_label = WT_expt_grp_hidden.label()
Df_label = Df_expt_grp_hidden.label()
labels = [WT_label, Df_label]
fig = plt.figure(figsize=(8.5, 11))
gs1 = plt.GridSpec(1, 1, top=0.9, bottom=0.7, left=0.1, right=0.20)
across_ctx_ax = fig.add_subplot(gs1[0, 0])
gs2 = plt.GridSpec(3, 1, top=0.9, bottom=0.7, left=0.25, right=0.35)
wt_pie_ax = fig.add_subplot(gs2[0, 0])
df_pie_ax = fig.add_subplot(gs2[1, 0])
shuffle_pie_ax = fig.add_subplot(gs2[2, 0])
pie_axs = (wt_pie_ax, df_pie_ax, shuffle_pie_ax)
gs3 = plt.GridSpec(1, 1, top=0.9, bottom=0.7, left=0.4, right=0.5)
cue_cell_bar_ax = fig.add_subplot(gs3[0, 0])
gs5 = plt.GridSpec(1, 1, top=0.5, bottom=0.3, left=0.1, right=0.3)
acute_stability_ax = fig.add_subplot(gs5[0, 0])
acute_stability_inset_ax = fig.add_axes([0.23, 0.32, 0.05, 0.08])
gs6 = plt.GridSpec(1, 1, top=0.5, bottom=0.3, left=0.4, right=0.5)
task_compare_ax = fig.add_subplot(gs6[0, 0])
#
# RF Compare
#
params = {}
params['filename'] = filename
params_cent_shift_pc = {}
params_cent_shift_pc['stability_fn'] = place.activity_centroid_shift
params_cent_shift_pc['stability_kwargs'] = {
'activity_filter': 'pc_both',
'circ_var_pcs': False,
'units': 'norm',
'shuffle': True
}
params_cent_shift_pc['stability_label'] = \
'Centroid shift (fraction of belt)'
params_cent_shift_all = {}
params_cent_shift_all['stability_fn'] = place.activity_centroid_shift
params_cent_shift_all['stability_kwargs'] = {
'activity_filter': 'active_both',
'circ_var_pcs': False,
'units': 'norm',
'shuffle': True
}
params_cent_shift_all['stability_label'] = \
'Centroid shift (fraction of belt)'
params_cent_shift_all['stability_inset_ylim'] = (0.15, 0.30)
params_cent_shift_all['stability_cdf_range'] = (0.15, 0.35)
params_cent_shift_all['stability_cdf_ticks'] = \
(0.15, 0.20, 0.25, 0.30, 0.35)
params_cent_shift_all['stability_compare_ylim'] = (0.15, 0.27)
params_cent_shift_all['stability_compare_yticks'] = (0.15, 0.20, 0.25)
params_cent_shift_all['ctx_compare_ylim'] = (0.10, 0.30)
params_cent_shift_all['ctx_compare_yticks'] = \
(0.10, 0.15, 0.20, 0.25, 0.30)
params_cent_shift_cm = {}
params_cent_shift_cm['stability_fn'] = place.activity_centroid_shift
params_cent_shift_cm['stability_kwargs'] = {
'activity_filter': 'active_both',
'circ_var_pcs': False,
'units': 'cm',
'shuffle': True
}
params_cent_shift_cm['stability_label'] = 'Centroid shift (cm)'
params_pop_vect_corr = {}
params_pop_vect_corr['stability_fn'] = place.population_vector_correlation
params_pop_vect_corr['stability_kwargs'] = {
'method': 'corr',
'activity_filter': 'pc_both',
'min_pf_density': 0.05,
'circ_var_pcs': False
}
params_pop_vect_corr['stability_label'] = 'Population vector correlation'
params_pf_corr = {}
params_pf_corr['stability_fn'] = place.place_field_correlation
params_pf_corr['stability_kwargs'] = {'activity_filter': 'pc_either'}
params_pf_corr['stability_label'] = 'Place field correlation'
params_pf_corr['stability_inset_ylim'] = (0, 0.50)
params_pf_corr['stability_cdf_range'] = (0.15, 0.55)
params_pf_corr['stability_cdf_ticks'] = (0.15, 0.25, 0.35, 0.45, 0.55)
params_pf_corr['stability_compare_ylim'] = (0.22, 0.40)
params_pf_corr['stability_compare_yticks'] = (0.25, 0.30, 0.35, 0.40)
params_pf_corr['hidden_ctx_compare_ylim'] = (0.22, 0.40)
params_pf_corr['hidden_ctx_compare_yticks'] = (0.25, 0.30, 0.35, 0.40)
params_pf_corr['ctx_compare_ylim'] = (0.22, 0.40)
params_pf_corr['ctx_compare_yticks'] = (0.25, 0.30, 0.35, 0.40)
params.update(params_cent_shift_all)
day_paired_grps_acute = [
grp.pair('consecutive groups', groupby=['day_in_df'])
for grp in expt_grps_acute
]
paired_grps_acute = day_paired_grps_acute
paired_grps_hidden = [
grp.pair('consecutive groups', groupby=['X_condition', 'X_day'])
for grp in expt_grps_hidden
]
filter_fn = lambda df: (df['expt_pair_label'] == 'SameAll')
filter_columns = ['expt_pair_label']
acute_stability = plotting.plot_metric(
acute_stability_ax,
paired_grps_acute,
metric_fn=params['stability_fn'],
groupby=[['expt_pair_label', 'second_expt']],
plotby=None,
plot_method='cdf',
plot_abs=True,
roi_filters=roi_filters,
activity_kwargs=params['stability_kwargs'],
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label=params['stability_label'],
colors=colors,
rotate_labels=False,
filter_fn=filter_fn,
filter_columns=filter_columns,
return_full_dataframes=False,
linestyles=linestyles)
acute_stability_ax.set_xlabel(params['stability_label'])
acute_stability_ax.set_title('')
sns.despine(ax=acute_stability_ax)
acute_stability_ax.set_xlim(params['stability_cdf_range'])
acute_stability_ax.set_xticks(params['stability_cdf_ticks'])
acute_stability_ax.legend(loc='upper left', fontsize=6)
plotting.plot_metric(acute_stability_inset_ax,
paired_grps_acute,
metric_fn=params['stability_fn'],
groupby=[['second_expt'], ['second_mouseID']],
plotby=None,
plot_method='swarm',
plot_abs=True,
roi_filters=roi_filters,
activity_kwargs=params['stability_kwargs'],
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label=params['stability_label'],
colors=colors,
rotate_labels=False,
filter_fn=filter_fn,
filter_columns=filter_columns,
linewidth=0.2,
edgecolor='gray',
plot_shuffle_as_hline=True)
acute_stability_inset_ax.get_legend().set_visible(False)
sns.despine(ax=acute_stability_inset_ax)
acute_stability_inset_ax.set_title('')
acute_stability_inset_ax.set_ylabel('')
acute_stability_inset_ax.set_xlabel('')
acute_stability_inset_ax.tick_params(bottom=False, labelbottom=False)
acute_stability_inset_ax.set_ylim(params['stability_inset_ylim'])
acute_stability_inset_ax.set_yticks(params['stability_inset_ylim'])
tmp_fig = plt.figure()
tmp_ax = tmp_fig.add_subplot(111)
hidden_stability = plotting.plot_metric(
tmp_ax,
paired_grps_hidden,
metric_fn=params['stability_fn'],
groupby=[['expt_pair_label', 'second_expt']],
plotby=('expt_pair_label', ),
plot_method='line',
plot_abs=True,
roi_filters=roi_filters,
activity_kwargs=params['stability_kwargs'],
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
activity_label=params['stability_label'],
colors=colors,
rotate_labels=False,
filter_fn=filter_fn,
filter_columns=filter_columns,
return_full_dataframes=False)
plt.close(tmp_fig)
wt_acute = acute_stability[WT_label]['dataframe']
wt_acute_shuffle = acute_stability[WT_label]['shuffle']
df_acute = acute_stability[Df_label]['dataframe']
df_acute_shuffle = acute_stability[Df_label]['shuffle']
wt_hidden = hidden_stability[WT_label]['dataframe']
wt_hidden_shuffle = hidden_stability[WT_label]['shuffle']
df_hidden = hidden_stability[Df_label]['dataframe']
df_hidden_shuffle = hidden_stability[Df_label]['shuffle']
for dataframe in (wt_acute, wt_acute_shuffle, df_acute, df_acute_shuffle):
dataframe['task'] = 'RF'
for dataframe in (wt_hidden, wt_hidden_shuffle, df_hidden,
df_hidden_shuffle):
dataframe['task'] = 'GOL'
WT_data = wt_acute.append(wt_hidden, ignore_index=True)
Df_data = df_acute.append(df_hidden, ignore_index=True)
WT_shuffle = wt_acute_shuffle.append(wt_hidden_shuffle, ignore_index=True)
Df_shuffle = df_acute_shuffle.append(df_hidden_shuffle, ignore_index=True)
filter_columns = ('expt_pair_label', )
filter_fn = lambda df: (df['expt_pair_label'] == 'SameAll')
order_dict = {'RF': 0, 'GOL': 1}
WT_data['order'] = WT_data['task'].map(order_dict)
Df_data['order'] = Df_data['task'].map(order_dict)
line_kwargs = {'markersize': 4}
plotting.plot_dataframe(task_compare_ax, [WT_data, Df_data],
[WT_shuffle, Df_shuffle],
labels=labels,
activity_label='',
groupby=[['task', 'second_mouseID']],
plotby=('task', ),
plot_method='box_and_line',
colors=colors,
filter_fn=filter_fn,
filter_columns=filter_columns,
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
orderby='order',
notch=False,
plot_shuffle_as_hline=True,
markers=markers,
linestyles=linestyles,
line_kwargs=line_kwargs,
flierprops={
'markersize': 3,
'marker': 'o'
},
whis='range')
task_compare_ax.set_title('')
sns.despine(ax=task_compare_ax)
task_compare_ax.set_ylim(params['stability_compare_ylim'])
task_compare_ax.set_yticks(params['stability_compare_yticks'])
task_compare_ax.set_xlabel('')
task_compare_ax.set_ylabel(params['stability_label'])
task_compare_ax.legend(loc='upper right', fontsize=6)
#
# Stability across transition
#
groupby = [['second_expt'], ['second_mouse']]
filter_fn = lambda df: (df['X_first_condition'] == 'A') \
& (df['X_second_condition'] == 'B')
filter_columns = ('X_first_condition', 'X_second_condition')
plotting.plot_metric(across_ctx_ax,
paired_grps_hidden,
metric_fn=params['stability_fn'],
groupby=groupby,
plotby=None,
plot_method='swarm',
activity_kwargs=params['stability_kwargs'],
plot_shuffle=True,
shuffle_plotby=False,
pool_shuffle=True,
colors=colors,
activity_label=params['stability_label'],
rotate_labels=False,
filter_fn=filter_fn,
filter_columns=filter_columns,
plot_shuffle_as_hline=True,
return_full_dataframes=False,
plot_bar=True,
roi_filters=roi_filters)
sns.despine(ax=across_ctx_ax)
across_ctx_ax.set_ylim(0.0, 0.3)
across_ctx_ax.set_yticks([0.0, 0.1, 0.2, 0.3])
across_ctx_ax.set_xticklabels([])
across_ctx_ax.set_xlabel('')
across_ctx_ax.set_title('')
across_ctx_ax.get_legend().set_visible(False)
plotting.stackedText(across_ctx_ax, labels, colors=colors, loc=2, size=10)
#
# Cue remapping
#
THRESHOLD = 0.05 * 2 * np.pi
CUENESS_THRESHOLD = 0.33
def first_cue_position(row):
expt = row['first_expt']
cue = row['cue']
cues = expt.belt().cues(normalized=True)
first_cue = cues.ix[cues['cue'] == cue]
pos = (first_cue['start'] + first_cue['stop']) / 2
angle = pos * 2 * np.pi
return np.complex(np.cos(angle), np.sin(angle))
def dotproduct(v1, v2):
return sum((a * b) for a, b in zip(v1, v2))
def length(v):
return math.sqrt(dotproduct(v, v))
def angle(v1, v2):
return math.acos(
np.round(dotproduct(v1, v2) / (length(v1) * length(v2)), 3))
def distance_to_first_cue(row):
centroid = row['second_centroid']
pos = row['first_cue_position']
return angle((pos.real, pos.imag), (centroid.real, centroid.imag))
WT_copy = copy(WT_expt_grp_hidden)
WT_copy.filterby(lambda df: ~df['X_condition'].str.contains('C'),
['X_condition'])
WT_paired = WT_copy.pair('consecutive groups',
groupby=['X_condition',
'X_day']).pair('consecutive groups',
groupby=['X_condition'])
Df_copy = copy(Df_expt_grp_hidden)
Df_copy.filterby(lambda df: ~df['X_condition'].str.contains('C'),
['X_condition'])
Df_paired = Df_copy.pair('consecutive groups',
groupby=['X_condition',
'X_day']).pair('consecutive groups',
groupby=['X_condition'])
WT_df, WT_shuffle_df = place.cue_cell_remapping(
WT_paired,
roi_filter=WT_filter,
near_threshold=THRESHOLD,
activity_filter='active_both',
circ_var_pcs=False,
shuffle=True)
Df_df, Df_shuffle_df = place.cue_cell_remapping(
Df_paired,
roi_filter=Df_filter,
near_threshold=THRESHOLD,
activity_filter='active_both',
circ_var_pcs=False,
shuffle=True)
shuffle_df = pd.concat([WT_shuffle_df, Df_shuffle_df], ignore_index=True)
cueness, cueness_fraction = [], []
cue_n, place_n, neither_n = [], [], []
for grp_df in (WT_df, Df_df, shuffle_df):
grp_df['first_cue_position'] = grp_df.apply(first_cue_position, axis=1)
grp_df['second_distance_to_first_cue_position'] = grp_df.apply(
distance_to_first_cue, axis=1)
grp_df['cueness'] = grp_df['second_distance_to_first_cue_position'] / \
(grp_df['value'] + grp_df['second_distance_to_first_cue_position'])
plotting.prepare_dataframe(grp_df, ['first_mouse'])
cueness_fraction.append([[]])
cue_n.append([])
place_n.append([])
neither_n.append([])
for mouse, mouse_df in grp_df.groupby('first_mouse'):
cue_n[-1].append((mouse_df['cueness'] >
(1 - CUENESS_THRESHOLD)).sum())
place_n[-1].append((mouse_df['cueness'] < CUENESS_THRESHOLD).sum())
neither_n[-1].append(mouse_df.shape[0] - cue_n[-1][-1] -
place_n[-1][-1])
cueness_fraction[-1][0].append(cue_n[-1][-1] /
float(place_n[-1][-1]))
cueness.append([grp_df['cueness']])
cue_labels = labels + ['shuffle']
plotting.swarm_plot(cue_cell_bar_ax,
cueness_fraction[:2],
condition_labels=labels,
colors=colors,
plot_bar=True)
cue_cell_bar_ax.axhline(np.mean(cueness_fraction[-1][0]),
ls='--',
color='k')
sns.despine(ax=cue_cell_bar_ax)
cue_cell_bar_ax.set_ylim(0, 1.5)
cue_cell_bar_ax.set_yticks([0, 0.5, 1.0, 1.5])
cue_cell_bar_ax.set_xticklabels([])
cue_cell_bar_ax.set_xlabel('')
cue_cell_bar_ax.set_ylabel('Cue-to-position ratio')
cue_cell_bar_ax.get_legend().set_visible(False)
plotting.stackedText(cue_cell_bar_ax,
labels,
colors=colors,
loc=2,
size=10)
WT_colors = sns.light_palette(WT_color, 7)[:-6:-2]
Df_colors = sns.light_palette(Df_color, 7)[:-6:-2]
shuffle_colors = sns.light_palette('k', 7)[:-6:-2]
pie_colors = (WT_colors, Df_colors, shuffle_colors)
pie_labels = ['cue', 'position', 'neither']
orig_size = mpl.rcParams.get('xtick.labelsize')
mpl.rcParams['xtick.labelsize'] = 5
for grp_ax, grp_label, grp_cue_n, grp_place_n, grp_neither_n, p_cs in zip(
pie_axs, cue_labels, cue_n, place_n, neither_n, pie_colors):
grp_ax.pie([sum(grp_cue_n),
sum(grp_place_n),
sum(grp_neither_n)],
autopct='%1.0f%%',
shadow=False,
frame=False,
labels=pie_labels,
colors=p_cs,
textprops={'fontsize': 5})
grp_ax.set_title(grp_label)
plotting.square_axis(grp_ax)
mpl.rcParams['xtick.labelsize'] = orig_size
misc.save_figure(fig, params['filename'], save_dir=save_dir)
plt.close('all')
def main():
all_grps = df.loadExptGrps('GOL')
WT_expt_grp = all_grps['WT_place_set']
Df_expt_grp = all_grps['Df_place_set']
expt_grps = [WT_expt_grp, Df_expt_grp]
fig, axs = plt.subplots(4,
3,
figsize=(8.5, 11),
gridspec_kw={
'wspace': 0.4,
'hspace': 0.3
})
#
# Velocity
#
plotting.plot_metric(axs[0, 0],
expt_grps,
metric_fn=lab.ExperimentGroup.velocity_dataframe,
groupby=[['expt'], ['mouseID']],
plotby=None,
plot_method='swarm',
activity_kwargs=None,
filter_fn=lambda df: df['condition'] == 'A',
filter_columns=['condition'],
activity_label='Velocity (cm/s)',
colors=colors,
plot_bar=True,
edgecolor='k',
linewidth=0.5,
return_full_dataframes=False)
plotting.plot_metric(axs[0, 1],
expt_grps,
metric_fn=lab.ExperimentGroup.velocity_dataframe,
groupby=[['expt'], ['session_in_day', 'mouseID']],
plotby=['session_in_day'],
plot_method='swarm',
activity_kwargs=None,
rotate_labels=False,
filter_fn=lambda df: df['condition'] == 'A',
filter_columns=['condition'],
activity_label='Velocity (cm/s)',
colors=colors,
plot_bar=True,
edgecolor='k',
linewidth=0.5)
#
# Lap Rate
#
plotting.plot_metric(axs[1, 0],
expt_grps,
metric_fn=lab.ExperimentGroup.number_of_laps,
groupby=[['expt'], ['mouseID']],
plotby=None,
plot_method='swarm',
activity_kwargs={'rate': True},
filter_fn=lambda df: df['condition'] == 'A',
filter_columns=['condition'],
activity_label='Lap rate (1/min)',
colors=colors,
agg_fn=[np.sum, np.mean],
plot_bar=True,
edgecolor='k',
linewidth=0.5,
return_full_dataframes=False)
plotting.plot_metric(axs[1, 1],
expt_grps,
metric_fn=lab.ExperimentGroup.number_of_laps,
groupby=[['expt'], ['session_in_day', 'mouseID']],
plotby=['session_in_day'],
plot_method='swarm',
activity_kwargs={'rate': True},
rotate_labels=False,
filter_fn=lambda df: df['condition'] == 'A',
filter_columns=['condition'],
activity_label='Lap rate (1/min)',
colors=colors,
agg_fn=[np.sum, np.mean],
plot_bar=True,
edgecolor='k',
linewidth=0.5)
#
# Lick Rate
#
plotting.plot_metric(axs[2, 0],
expt_grps,
metric_fn=lab.ExperimentGroup.behavior_dataframe,
groupby=[['trial'], ['mouseID']],
plotby=None,
plot_method='swarm',
activity_kwargs={
'key': 'licking',
'rate': True
},
filter_fn=lambda df: df['condition'] == 'A',
filter_columns=['condition'],
activity_label='Lick rate (Hz)',
colors=colors,
agg_fn=[np.sum, np.mean],
plot_bar=True,
edgecolor='k',
linewidth=0.5,
return_full_dataframes=False)
plotting.plot_metric(axs[2, 1],
expt_grps,
metric_fn=lab.ExperimentGroup.behavior_dataframe,
groupby=[['trial'], ['session_in_day', 'mouseID']],
plotby=['session_in_day'],
plot_method='swarm',
roi_filters=None,
activity_kwargs={
'key': 'licking',
'rate': True
},
filter_fn=lambda df: df['condition'] == 'A',
filter_columns=['condition'],
activity_label='Lick rate (Hz)',
colors=colors,
agg_fn=[np.sum, np.mean],
rotate_labels=False,
plot_bar=True,
edgecolor='k',
linewidth=0.5)
for ax in axs[3, :]:
ax.set_visible(False)
for ax in axs[:, 2]:
ax.set_visible(False)
sns.despine(fig=fig)
for ax in axs.flat:
ax.set_title('')
for ax in axs[:, 0]:
ax.set_xlabel('')
ax.tick_params(bottom=False, labelbottom=False, length=3, pad=2)
for ax in axs[:, 1]:
ax.set_xlabel('')
ax.set_ylabel('')
ax.set_xticklabels(['1', '2', '3'])
ax.tick_params(length=3, pad=2)
for ax in axs[:3, :2].flat:
ax.get_legend().set_visible(False)
plotting.stackedText(axs[0, 0], [WT_label, Df_label],
colors=colors,
loc=2,
size=10)
axs[2, 1].set_xlabel('Session in day')
for ax in axs[0, :]:
ax.set_ylim(0, 13)
for ax in axs[1, :]:
ax.set_ylim(0, 2.0)
ax.set_yticks([0, 0.5, 1.0, 1.5, 2.0])
for ax in axs[2, :]:
ax.set_ylim(0, 3)
misc.save_figure(fig, filename, save_dir=save_dir)
plt.close('all')
def main():
all_grps = df.loadExptGrps('GOL')
expts = lab.ExperimentSet(os.path.join(df.metadata_path,
'expt_metadata.xml'),
behaviorDataPath=os.path.join(
df.data_path, 'behavior'),
dataPath=os.path.join(df.data_path, 'imaging'))
WT_expt_grp = all_grps['WT_place_set']
Df_expt_grp = all_grps['Df_place_set']
expt_grps = [WT_expt_grp, Df_expt_grp]
WT_label = WT_expt_grp.label()
Df_label = Df_expt_grp.label()
fig = plt.figure(figsize=(8.5, 11))
gs2 = plt.GridSpec(48, 1, right=.6)
wt_trace_ax = fig.add_subplot(gs2[12:16, 0])
wt_position_ax = fig.add_subplot(gs2[16:18, 0])
df_trace_ax = fig.add_subplot(gs2[18:22, 0])
df_position_ax = fig.add_subplot(gs2[22:24, 0])
gs3 = plt.GridSpec(2, 2, hspace=0.3, left=.62, bottom=0.5, top=0.7)
wt_transients_ax = fig.add_subplot(gs3[0, 0], polar=True)
df_transients_ax = fig.add_subplot(gs3[1, 0], polar=True)
wt_vector_ax = fig.add_subplot(gs3[0, 1], polar=True)
df_vector_ax = fig.add_subplot(gs3[1, 1], polar=True)
gs4 = plt.GridSpec(1, 4, top=0.48, bottom=0.35, wspace=0.3)
pf_fraction_ax = fig.add_subplot(gs4[0, 0])
pf_per_cell_ax = fig.add_subplot(gs4[0, 1])
pf_width_ax = fig.add_subplot(gs4[0, 2])
circ_var_ax = fig.add_subplot(gs4[0, 3])
pf_fraction_inset_ax = fig.add_axes([0.22, 0.36, 0.04, 0.06])
pf_width_inset_ax = fig.add_axes([0.63, 0.41, 0.04, 0.06])
circ_var_inset_ax = fig.add_axes([0.84, 0.36, 0.04, 0.06])
#
# PC Examples
#
wt_expt = expts.grabExpt('jz121', '2015-02-21-16h06m30s')
df_expt = expts.grabExpt('jz098', '2014-11-08-16h14m02s')
pc_expt_grp = place.pcExperimentGroup([wt_expt, df_expt],
imaging_label='soma')
wt_id = '0422-0349'
df_id = '0074-0339'
wt_idx = wt_expt.roi_ids().index(wt_id)
df_idx = df_expt.roi_ids().index(df_id)
wt_imaging_data = wt_expt.imagingData(channel='Ch2',
label='soma',
dFOverF='from_file')
df_imaging_data = df_expt.imagingData(channel='Ch2',
label='soma',
dFOverF='from_file')
wt_transients = wt_expt.transientsData(threshold=95,
channel='Ch2',
label='soma')
df_transients = df_expt.transientsData(threshold=95,
channel='Ch2',
label='soma')
place.plotImagingData(roi_tSeries=wt_imaging_data[wt_idx, :, 0],
ax=wt_trace_ax,
roi_transients=wt_transients[wt_idx][0],
position=None,
imaging_interval=wt_expt.frame_period(),
placeField=None,
xlabel_visible=False,
ylabel_visible=True,
right_label=True,
placeFieldColor=None,
title='',
rasterized=False,
color='.4',
transients_color=WT_color)
sns.despine(ax=wt_trace_ax, top=True, left=False, bottom=True, right=True)
wt_trace_ax.set_ylabel(WT_label, rotation='horizontal', ha='right')
wt_trace_ax.tick_params(bottom=False, labelbottom=False)
wt_trace_ax.tick_params(axis='y', direction='in', length=3, pad=3)
wt_trace_ax.spines['left'].set_linewidth(1)
wt_trace_ax.spines['left'].set_position(('outward', 5))
place.plotImagingData(roi_tSeries=df_imaging_data[df_idx, :, 0],
ax=df_trace_ax,
roi_transients=df_transients[df_idx][0],
position=None,
imaging_interval=df_expt.frame_period(),
placeField=None,
xlabel_visible=False,
ylabel_visible=True,
right_label=True,
placeFieldColor=None,
title='',
rasterized=False,
color='.4',
transients_color=Df_color)
sns.despine(ax=df_trace_ax, top=True, left=False, bottom=True, right=True)
df_trace_ax.set_ylabel(Df_label, rotation='horizontal', ha='right')
df_trace_ax.tick_params(bottom=False, labelbottom=False)
df_trace_ax.tick_params(axis='y', direction='in', length=3, pad=3)
df_trace_ax.spines['left'].set_linewidth(1)
df_trace_ax.spines['left'].set_position(('outward', 5))
y_min = min(wt_trace_ax.get_ylim()[0], df_trace_ax.get_ylim()[0])
y_max = max(wt_trace_ax.get_ylim()[1], df_trace_ax.get_ylim()[1])
wt_trace_ax.set_ylim(y_min, y_max)
df_trace_ax.set_ylim(y_min, y_max)
wt_trace_ax.set_yticks([0, y_max])
df_trace_ax.set_yticks([0, y_max])
wt_trace_ax.set_yticklabels(['0', '{:0.1f}'.format(y_max)])
df_trace_ax.set_yticklabels(['0', '{:0.1f}'.format(y_max)])
wt_trace_ax.set_xlim(0, 600)
df_trace_ax.set_xlim(0, 600)
place.plotPosition(wt_expt.find('trial'),
ax=wt_position_ax,
rasterized=False,
position_kwargs={'color': 'k'})
sns.despine(ax=wt_position_ax,
top=True,
left=True,
bottom=True,
right=True)
wt_position_ax.set_ylabel('')
wt_position_ax.set_xlabel('')
wt_position_ax.tick_params(left=False,
bottom=False,
top=False,
right=False,
labelleft=False,
labelbottom=False,
labelright=False,
labeltop=False)
plotting.add_scalebar(wt_position_ax,
matchx=False,
matchy=False,
hidex=False,
hidey=False,
sizex=60,
labelx='1 min',
bar_thickness=.02,
pad=0,
loc=4)
wt_position_ax.set_yticks([0, 1])
wt_position_ax.set_ylim(0, 1)
place.plotPosition(df_expt.find('trial'),
ax=df_position_ax,
rasterized=False,
position_kwargs={'color': 'k'})
sns.despine(ax=df_position_ax, top=True, bottom=True, right=True)
df_position_ax.tick_params(bottom=False,
top=False,
right=False,
labelbottom=False,
labelright=False,
labeltop=False,
direction='in',
length=3,
pad=3)
df_position_ax.spines['left'].set_linewidth(1)
df_position_ax.spines['left'].set_position(('outward', 5))
df_position_ax.set_ylabel('Position')
df_position_ax.set_xlabel('')
df_position_ax.set_yticks([0, 1])
df_position_ax.set_ylim(0, 1)
trans_kwargs = {
'color': WT_color,
'marker': 'o',
'linestyle': 'None',
'markersize': 3
}
wt_pf = [pc_expt_grp.pfs_n()[wt_expt][wt_idx]]
place.plotPosition(wt_expt.find('trial'),
ax=wt_transients_ax,
polar=True,
placeFields=wt_pf,
placeFieldColors=[WT_color],
trans_roi_filter=lambda roi: roi.id == wt_id,
rasterized=False,
running_trans_only=True,
demixed=False,
position_kwargs={'color': '0.5'},
trans_kwargs=trans_kwargs)
wt_transients_ax.set_xlabel('')
wt_transients_ax.set_ylabel('')
wt_transients_ax.set_rticks([])
prep_polar_ax(wt_transients_ax)
trans_kwargs['color'] = Df_color
df_pf = [pc_expt_grp.pfs_n()[df_expt][df_idx]]
place.plotPosition(df_expt.find('trial'),
ax=df_transients_ax,
polar=True,
placeFields=df_pf,
placeFieldColors=[Df_color],
trans_roi_filter=lambda roi: roi.id == df_id,
rasterized=False,
running_trans_only=True,
demixed=False,
position_kwargs={'color': '0.5'},
trans_kwargs=trans_kwargs)
df_transients_ax.set_xlabel('')
df_transients_ax.set_ylabel('')
df_transients_ax.set_rticks([])
prep_polar_ax(df_transients_ax)
place.plotTransientVectors(place.pcExperimentGroup([wt_expt],
imaging_label='soma'),
wt_idx,
wt_vector_ax,
mean_zorder=99,
color=WT_color,
mean_color='g')
place.plotTransientVectors(place.pcExperimentGroup([df_expt],
imaging_label='soma'),
df_idx,
df_vector_ax,
mean_zorder=99,
color=Df_color,
mean_color='g')
#
# Stats
#
groupby = [['expt'], ['mouseID']]
plotting.plot_metric(pf_fraction_ax,
expt_grps,
metric_fn=place.place_cell_percentage,
groupby=None,
plotby=None,
colorby=None,
plot_method='cdf',
roi_filters=roi_filters,
activity_kwargs=None,
colors=colors,
activity_label='Place cell fraction',
rotate_labels=False,
return_full_dataframes=False,
linestyles=linestyles)
pf_fraction_ax.legend(loc='upper left', fontsize=6)
pf_fraction_ax.set_title('')
pf_fraction_ax.set_ylabel('Cumulative fraction')
pf_fraction_ax.set_xticks([0, .2, .4, .6, .8])
pf_fraction_ax.set_xlim(0, .8)
pf_fraction_ax.spines['left'].set_linewidth(1)
pf_fraction_ax.spines['bottom'].set_linewidth(1)
plotting.plot_metric(pf_fraction_inset_ax,
expt_grps,
metric_fn=place.place_cell_percentage,
groupby=groupby,
plotby=None,
colorby=None,
plot_method='swarm',
roi_filters=roi_filters,
activity_kwargs=None,
colors=colors,
activity_label='Place cell fraction',
rotate_labels=False,
linewidth=0.2,
edgecolor='gray')
pf_fraction_inset_ax.set_title('')
pf_fraction_inset_ax.set_ylabel('')
pf_fraction_inset_ax.set_xlabel('')
pf_fraction_inset_ax.set_yticks([0, 0.5])
pf_fraction_inset_ax.set_ylim([0, 0.5])
pf_fraction_inset_ax.get_legend().set_visible(False)
sns.despine(ax=pf_fraction_inset_ax)
pf_fraction_inset_ax.tick_params(bottom=False, labelbottom=False)
pf_fraction_inset_ax.spines['left'].set_linewidth(1)
pf_fraction_inset_ax.spines['bottom'].set_linewidth(1)
pf_fraction_inset_ax.set_xlim(-0.6, 0.6)
n_pf_kwargs = {'per_mouse_fractions': True, 'max_n_place_fields': 3}
plotting.plot_metric(pf_per_cell_ax,
expt_grps,
metric_fn=place.n_place_fields,
groupby=None,
plotby=['number'],
plot_method='swarm',
roi_filters=roi_filters,
activity_kwargs=n_pf_kwargs,
colors=colors,
activity_label='Fraction of place cells',
rotate_labels=False,
plot_bar=True,
edgecolor='k',
linewidth=0.5,
size=3)
sns.despine(ax=pf_per_cell_ax)
pf_per_cell_ax.set_title('')
pf_per_cell_ax.set_xlabel('Place fields per cell')
pf_per_cell_ax.set_ylabel('Fraction of place cells')
pf_per_cell_ax.set_xticklabels(['1', '2', '3+'])
pf_per_cell_ax.set_yticks([0, 0.2, 0.4, 0.6, 0.8, 1])
plotting.plot_metric(pf_width_ax,
expt_grps,
metric_fn=place.place_field_width,
groupby=[['roi_id', 'expt']],
plotby=None,
plot_method='hist',
roi_filters=roi_filters,
activity_kwargs=None,
activity_label='Place field width (cm)',
normed=True,
plot_mean=True,
bins=20,
range=(0, 120),
colors=colors,
rotate_labels=False,
filled=False,
mean_kwargs={'ls': ':'},
return_full_dataframes=False,
linestyles=linestyles)
pf_width_ax.set_title('')
pf_width_ax.legend(loc='lower right', fontsize=6)
pf_width_ax.set_xticks([0, 40, 80, 120])
pf_width_ax.set_yticks([0, 0.02, 0.04, 0.06, 0.08])
pf_width_ax.set_ylim(0, 0.08)
pf_width_ax.set_ylabel('Normalized density')
pf_width_ax.spines['left'].set_linewidth(1)
pf_width_ax.spines['bottom'].set_linewidth(1)
plotting.plot_metric(pf_width_inset_ax,
expt_grps,
metric_fn=place.place_field_width,
groupby=[['roi_id', 'expt'], ['expt'], ['mouseID']],
plotby=None,
plot_method='swarm',
roi_filters=roi_filters,
activity_kwargs=None,
activity_label='Place field width (cm)',
colors=colors,
rotate_labels=False,
linewidth=0.2,
edgecolor='gray')
pf_width_inset_ax.set_title('')
pf_width_inset_ax.set_ylabel('')
pf_width_inset_ax.set_xlabel('')
pf_width_inset_ax.get_legend().set_visible(False)
sns.despine(ax=pf_width_inset_ax)
pf_width_inset_ax.tick_params(bottom=False, labelbottom=False)
pf_width_inset_ax.set_ylim(25, 40)
pf_width_inset_ax.set_yticks([25, 40])
pf_width_inset_ax.spines['left'].set_linewidth(1)
pf_width_inset_ax.spines['bottom'].set_linewidth(1)
pf_width_inset_ax.set_xlim(-0.6, 0.6)
plotting.plot_metric(circ_var_ax,
expt_grps,
metric_fn=place.circular_variance,
groupby=[['roi_id', 'expt']],
plotby=None,
plot_method='cdf',
roi_filters=roi_filters,
activity_kwargs=None,
activity_label='Circular variance',
colors=colors,
rotate_labels=False,
return_full_dataframes=False,
linestyles=linestyles)
circ_var_ax.set_title('')
circ_var_ax.legend(loc='upper left', fontsize=6)
circ_var_ax.set_ylabel('Cumulative fraction')
circ_var_ax.set_xlim(-0.1, 1)
circ_var_ax.set_xticks([0, 0.5, 1])
circ_var_ax.spines['left'].set_linewidth(1)
circ_var_ax.spines['bottom'].set_linewidth(1)
plotting.plot_metric(circ_var_inset_ax,
expt_grps,
metric_fn=place.circular_variance,
groupby=groupby,
plotby=None,
plot_method='swarm',
roi_filters=roi_filters,
activity_kwargs=None,
activity_label='Circular variance',
colors=colors,
rotate_labels=False,
linewidth=0.2,
edgecolor='gray')
circ_var_inset_ax.set_title('')
circ_var_inset_ax.set_ylabel('')
circ_var_inset_ax.set_xlabel('')
circ_var_inset_ax.get_legend().set_visible(False)
sns.despine(ax=circ_var_inset_ax)
circ_var_inset_ax.tick_params(bottom=False, labelbottom=False)
circ_var_inset_ax.set_ylim(0, 0.6)
circ_var_inset_ax.set_yticks([0, 0.6])
circ_var_inset_ax.spines['left'].set_linewidth(1)
circ_var_inset_ax.spines['bottom'].set_linewidth(1)
circ_var_inset_ax.set_xlim(-0.6, 0.6)
misc.save_figure(fig, filename, save_dir=save_dir)
plt.close('all')
def main():
all_expt_grps = df.loadExptGrps('GOL')
WT_expt_grp_hidden = all_expt_grps['WT_place_set']
Df_expt_grp_hidden = all_expt_grps['Df_place_set']
expt_grps = [WT_expt_grp_hidden, Df_expt_grp_hidden]
paired_grps = [grp.pair(
'consecutive groups', groupby=['condition_day']) for grp in expt_grps]
fig = plt.figure(figsize=(8.5, 11))
gs1 = plt.GridSpec(
3, 8, top=0.9, bottom=0.7, left=0.1, right=0.9, wspace=0.4)
ax2 = fig.add_subplot(gs1[:, :2])
pf_fraction_ax = fig.add_subplot(gs1[:, 2:4])
circ_var_ax = fig.add_subplot(gs1[:, 4:6])
trans_ax1 = fig.add_subplot(gs1[0, 6], polar=True)
trans_ax2 = fig.add_subplot(gs1[0, 7], polar=True)
trans_ax3 = fig.add_subplot(gs1[1, 6], polar=True)
trans_ax4 = fig.add_subplot(gs1[1, 7], polar=True)
trans_ax5 = fig.add_subplot(gs1[2, 6], polar=True)
trans_ax6 = fig.add_subplot(gs1[2, 7], polar=True)
trans_axs = [
trans_ax1, trans_ax2, trans_ax3, trans_ax4, trans_ax5, trans_ax6]
#
# Stability by distance to fabric transitions
#
filter_fn = lambda df: df['second_condition_day_session'] == 'B_0_0'
filter_columns = ['second_condition_day_session']
label_order = ['before', 'middle', 'after']
data_to_plot = [[], [], []]
all_data, shuffles = [], []
for expt_grp, roi_filter in zip(paired_grps, roi_filters):
fabric_map = {expt: expt.belt().fabric_transitions(
units='normalized') for expt in expt_grp}
def norm_diff(n1, n2):
d = n1 - n2
d = d + 1.0 if d < -0.5 else d
d = d - 1.0 if d >= 0.5 else d
return d
def closest_transition(row):
expt = row['first_expt']
centroid = complex_to_norm(row['first_centroid'])
positions = fabric_map[expt]['position']
distances = [norm_diff(centroid, t) for t in positions]
row['closest'] = distances[np.argmin(np.abs(distances))]
return row
data, shuffle = place.activity_centroid_shift(
expt_grp, roi_filter=roi_filter, activity_filter='active_both',
circ_var_pcs=False, units='norm', shuffle=True)
plotting.prepare_dataframe(data, include_columns=filter_columns)
data = data[filter_fn(data)]
plotting.prepare_dataframe(shuffle, include_columns=filter_columns)
data = data.apply(closest_transition, axis=1)
shuffle = shuffle.apply(closest_transition, axis=1)
def categorize(row):
if row['closest'] < 0 and -1 / 9. < row['closest']:
row['category'] = 'before'
elif row['closest'] > 0 and 1 / 9. > row['closest']:
row['category'] = 'after'
else:
row['category'] = 'middle'
return row
data = data.apply(categorize, axis=1)
shuffle = shuffle.apply(categorize, axis=1)
groupby = [
['second_condition_day_session', 'second_mouse', 'category']]
for gb in groupby:
plotting.prepare_dataframe(data, include_columns=gb)
plotting.prepare_dataframe(shuffle, include_columns=gb)
data = data.groupby(gb, as_index=False).mean()
shuffle = shuffle.groupby(gb, as_index=False).mean()
for category, group in data.groupby(['category']):
idx = label_order.index(category)
data_to_plot[idx].append(group['value'])
shuffles.append(shuffle)
all_data.append(data)
shuffle_df = pd.concat(shuffles, ignore_index=True)
for category, group in shuffle_df.groupby(['category']):
idx = label_order.index(category)
data_to_plot[idx].append(group['value'])
plotting.grouped_bar(
ax2, data_to_plot, condition_labels=label_order,
cluster_labels=df.labels + ('shuffle',),
bar_colors=sns.color_palette('deep')[3:], scatter_points=False,
scatterbar_colors=None, jitter_x=False, loc='best', error_bars='sem')
sns.despine(ax=ax2)
ax2.set_yticks([0, 0.1, 0.2, 0.3])
ax2.set_ylabel('Centroid shift (fraction of belt)')
#
# Burlap belt
#
expts = lab.ExperimentSet(
os.path.join(df.metadata_path, 'expt_metadata.xml'),
behaviorDataPath=os.path.join(df.data_path, 'behavior'),
dataPath=os.path.join(df.data_path, 'imaging'))
burlap_expt_grp = lab.classes.pcExperimentGroup.from_json(
cue_free_json, expts, imaging_label=df.IMAGING_LABEL, label='cue-free')
acute_grps = df.loadExptGrps('RF')
WT_expt_grp_acute = acute_grps['WT_place_set'].unpair()
WT_expt_grp_acute.label('cue-rich')
burlap_colors = ('k', '0.9')
example_expt = expts.grabExptByPath('/jz128/TSeries-07262015-burlap-000')
cv = place.circular_variance_p(burlap_expt_grp)
cv = cv[cv['expt'] == example_expt]
cv = cv.sort_values(by=['value'])
trans_kwargs = {
'color': '0.9', 'marker': 'o', 'linestyle': 'None',
'markersize': 3}
for ax, (idx, row) in zip(trans_axs, cv.iloc[:6].iterrows()):
expt = row['expt']
roi_idx = expt.rois().index(row['roi'])
pf = None
place.plotPosition(
expt.find('trial'), ax=ax, polar=True,
placeFields=pf, placeFieldColors=['0.9'],
trans_roi_filter=lambda roi: roi.id == expt.roi_ids()[roi_idx],
rasterized=False, running_trans_only=True, demixed=False,
position_kwargs={'color': '0.5'}, trans_kwargs=trans_kwargs)
ax.set_xlabel('')
ax.set_ylabel('')
ax.set_rticks([])
prep_polar_ax(ax)
for ax in trans_axs[:-1]:
ax.set_xticklabels(['', '', '', ''])
activity_kwargs = {'circ_var': True}
plotting.plot_metric(
pf_fraction_ax, [WT_expt_grp_acute, burlap_expt_grp],
metric_fn=place.place_cell_percentage,
groupby=None, plotby=None, colorby=None, plot_method='swarm',
roi_filters=[WT_filter, WT_filter], activity_kwargs=activity_kwargs,
colors=burlap_colors, activity_label='Place cell fraction',
rotate_labels=False, plot_bar=True)
pf_fraction_ax.set_title('')
pf_fraction_ax.set_xlabel('')
sns.despine(ax=pf_fraction_ax)
pf_fraction_ax.set_yticks([0.0, 0.1, 0.2, 0.3, 0.4])
plotting.plot_metric(
circ_var_ax, [WT_expt_grp_acute, burlap_expt_grp],
metric_fn=place.circular_variance,
groupby=[['roi_id', 'expt']], plotby=None, plot_method='cdf',
roi_filters=[WT_filter, WT_filter], activity_kwargs=None,
activity_label='Circular variance', colors=burlap_colors,
rotate_labels=False)
circ_var_ax.set_title('')
circ_var_ax.get_legend().set_visible(False)
circ_var_ax.set_xticks([0, 0.5, 1])
save_figure(fig, filename, save_dir=save_dir)
plt.close('all')
def main():
all_grps = df.loadExptGrps('GOL')
expts = lab.ExperimentSet(os.path.join(df.metadata_path,
'expt_metadata.xml'),
behaviorDataPath=os.path.join(
df.data_path, 'behavior'),
dataPath=os.path.join(df.data_path, 'imaging'))
WT_expt_grp = all_grps['WT_hidden_behavior_set']
Df_expt_grp = all_grps['Df_hidden_behavior_set']
expt_grps = [WT_expt_grp, Df_expt_grp]
if MALES_ONLY:
for expt_grp in expt_grps:
expt_grp.filter(lambda expt: expt.parent.get('sex') == 'M')
labels = [expt_grp.label() for expt_grp in expt_grps]
fig = plt.figure(figsize=(8.5, 11))
HORIZONTAL = False
if HORIZONTAL:
gs1 = plt.GridSpec(8, 6)
wt_lick_axs = [
fig.add_subplot(gs1[0, 0]),
fig.add_subplot(gs1[0, 1]),
fig.add_subplot(gs1[0, 2]),
fig.add_subplot(gs1[0, 3]),
fig.add_subplot(gs1[0, 4]),
fig.add_subplot(gs1[0, 5])
]
df_lick_axs = [
fig.add_subplot(gs1[1, 0]),
fig.add_subplot(gs1[1, 1]),
fig.add_subplot(gs1[1, 2]),
fig.add_subplot(gs1[1, 3]),
fig.add_subplot(gs1[1, 4]),
fig.add_subplot(gs1[1, 5])
]
gs2 = plt.GridSpec(4, 2, hspace=0.5, wspace=0.2)
reward_zone_ax = fig.add_subplot(gs2[1, 0])
else:
gs1 = plt.GridSpec(10, 6)
wt_lick_axs = [
fig.add_subplot(gs1[0, 0]),
fig.add_subplot(gs1[1, 0]),
fig.add_subplot(gs1[2, 0]),
fig.add_subplot(gs1[3, 0]),
fig.add_subplot(gs1[4, 0]),
fig.add_subplot(gs1[5, 0])
]
df_lick_axs = [
fig.add_subplot(gs1[0, 1]),
fig.add_subplot(gs1[1, 1]),
fig.add_subplot(gs1[2, 1]),
fig.add_subplot(gs1[3, 1]),
fig.add_subplot(gs1[4, 1]),
fig.add_subplot(gs1[5, 1])
]
gs2 = plt.GridSpec(10, 1, hspace=0.5, wspace=0.8, left=0.47, right=0.9)
reward_zone_ax = fig.add_subplot(gs2[0:4, :])
gs3 = plt.GridSpec(10, 3, hspace=0.5, wspace=0.1, left=0.47, right=0.9)
fraction_licks_by_session_A_ax = fig.add_subplot(gs3[5:7, 0])
fraction_licks_by_session_B_ax = fig.add_subplot(gs3[5:7, 1])
fraction_licks_by_session_C_ax = fig.add_subplot(gs3[5:7, 2])
#
# Lick plots
#
wt_lick_expts = [
expts.grabExpt('jz101', '2014-11-06-23h37m54s'),
expts.grabExpt('jz101', '2014-11-08-22h53m27s'),
expts.grabExpt('jz101', '2014-11-09-23h06m56s'),
expts.grabExpt('jz101', '2014-11-11-23h13m16s'),
expts.grabExpt('jz101', '2014-11-12-19h29m41s'),
expts.grabExpt('jz101', '2014-11-14-19h59m09s')
]
df_lick_expts = [
expts.grabExpt('jz106', '2014-12-11-17h06m49s'),
expts.grabExpt('jz106', '2014-12-13-19h00m01s'),
expts.grabExpt('jz106', '2014-12-14-17h17m17s'),
expts.grabExpt('jz106', '2014-12-16-17h43m05s'),
expts.grabExpt('jz106', '2014-12-17-17h57m51s'),
expts.grabExpt('jz106', '2014-12-19-17h13m52s')
]
shade_color = sns.xkcd_rgb['light green']
for ax, expt in zip(wt_lick_axs, wt_lick_expts):
expt.licktogram(ax=ax,
plot_belt=False,
nPositionBins=20,
color=WT_color,
linewidth=0,
shade_reward=True,
shade_color=shade_color)
for ax, expt in zip(df_lick_axs, df_lick_expts):
expt.licktogram(ax=ax,
plot_belt=False,
nPositionBins=20,
color=Df_color,
linewidth=0,
shade_reward=True,
shade_color=shade_color)
for ax in wt_lick_axs + df_lick_axs:
ax.set_ylim(0, 0.6)
ax.set_yticks([0, 0.3, 0.6])
ax.set_xticks([0, 0.5, 1])
ax.set_xticklabels(['0.0', '0.5', '1.0'])
sns.despine(ax=ax)
ax.set_title('')
if HORIZONTAL:
for ax in wt_lick_axs:
ax.tick_params(labelbottom=False)
ax.set_xlabel('')
for ax in df_lick_axs[1:]:
ax.set_xlabel('')
for ax, label in zip(wt_lick_axs, [
r'Condition $\mathrm{I}$' + '\nDay 1',
r'Condition $\mathrm{I}$' + '\nDay 3',
r'Condition $\mathrm{II}$' + '\nDay 1',
r'Condition $\mathrm{II}$' + '\nDay 3',
r'Condition $\mathrm{III}$' + '\nDay 1',
r'Condition $\mathrm{III}$' + '\nDay 3'
]):
ax.set_title(label)
for ax in it.chain(wt_lick_axs[1:], df_lick_axs[1:]):
ax.set_ylabel('')
sns.despine(ax=ax, left=True, top=True, right=True)
for ax in wt_lick_axs + df_lick_axs:
ax.spines['bottom'].set_linewidth(0.5)
wt_lick_axs[0].tick_params(labelbottom=False)
for ax in wt_lick_axs[1:]:
ax.tick_params(labelleft=False, left=False, labelbottom=False)
for ax in df_lick_axs[1:]:
ax.tick_params(labelleft=False, left=False)
right_label(wt_lick_axs[-1], labels[0])
right_label(df_lick_axs[-1], labels[1])
df_lick_axs[0].set_yticks([0, 0.6])
wt_lick_axs[0].set_yticks([0, 0.6])
df_lick_axs[0].set_ylabel('Fraction of licks')
wt_lick_axs[0].set_ylabel('')
df_lick_axs[0].spines['left'].set_linewidth(0.5)
wt_lick_axs[0].spines['left'].set_linewidth(0.5)
else:
for ax in wt_lick_axs + df_lick_axs:
ax.spines['bottom'].set_linewidth(0.5)
for ax in wt_lick_axs + df_lick_axs[1:]:
sns.despine(ax=ax, left=True, top=True, right=True)
sns.despine(ax=df_lick_axs[0], left=True, top=True, right=False)
for ax in wt_lick_axs[:-1] + df_lick_axs[:-1]:
ax.set_xlabel('')
for ax in df_lick_axs:
ax.set_ylabel('')
for ax, label in zip(wt_lick_axs, [
r'Condition $\mathrm{I}$' + '\nDay 1',
r'Condition $\mathrm{I}$' + '\nDay 3',
r'Condition $\mathrm{II}$' + '\nDay 1',
r'Condition $\mathrm{II}$' + '\nDay 3',
r'Condition $\mathrm{III}$' + '\nDay 1',
r'Condition $\mathrm{III}$' + '\nDay 3'
]):
ax.set_ylabel(label,
rotation='horizontal',
ha='right',
multialignment='center',
labelpad=3,
va='center')
for ax in wt_lick_axs[:-1] + df_lick_axs[:-1]:
ax.tick_params(labelleft=False, left=False, labelbottom=False)
for ax in (wt_lick_axs[-1], df_lick_axs[-1]):
ax.tick_params(labelleft=False, left=False)
wt_lick_axs[0].set_title(labels[0])
df_lick_axs[0].set_title(labels[1])
df_lick_axs[0].yaxis.tick_right()
df_lick_axs[0].yaxis.set_label_position("right")
df_lick_axs[0].set_yticks([0, 0.6])
df_lick_axs[0].tick_params(axis='y', length=2, pad=2, direction='in')
df_lick_axs[0].set_ylabel('Fraction of licks')
df_lick_axs[0].spines['right'].set_linewidth(0.5)
filter_fn = None
filter_columns = None
behavior_fn = ra.fraction_licks_in_reward_zone
behavior_kwargs = {}
activity_label = 'Fraction of licks in reward zone'
plot_metric(reward_zone_ax,
expt_grps,
metric_fn=behavior_fn,
activity_kwargs=behavior_kwargs,
groupby=[['expt'], ['mouseID', 'X_condition', 'X_day']],
plotby=['X_condition', 'X_day'],
plot_method='line',
activity_label=activity_label,
colors=colors,
linestyles=linestyles,
label_every_n=1,
label_groupby=False,
markers=markers,
markersize=5,
rotate_labels=False,
filter_fn=filter_fn,
filter_columns=filter_columns,
return_full_dataframes=False)
reward_zone_ax.set_yticks([0, .1, .2, .3, .4])
sns.despine(ax=reward_zone_ax)
reward_zone_ax.set_xlabel('Day in Condition')
reward_zone_ax.set_title('')
day_number_only_label(reward_zone_ax)
label_conditions(reward_zone_ax)
reward_zone_ax.legend(loc='lower left', fontsize=8)
# reward_zone_ax.get_legend().set_visible(False)
# stackedText(reward_zone_ax, labels, colors=colors, loc=3, size=10)
groupby = [['expt']]
plotby = ['X_condition', 'X_session']
filter_fn = lambda df: (df['X_session'] != '1') & (df['X_condition'] == 'A'
)
filter_columns = ['X_session', 'X_condition']
line_kwargs = {'markersize': 4}
plot_metric(fraction_licks_by_session_A_ax,
expt_grps,
metric_fn=behavior_fn,
activity_kwargs=behavior_kwargs,
groupby=groupby,
plotby=plotby,
plot_method='box_and_line',
activity_label=activity_label,
colors=colors,
notch=False,
label_every_n=1,
label_groupby=False,
markers=markers,
rotate_labels=False,
line_kwargs=line_kwargs,
linestyles=linestyles,
filter_fn=filter_fn,
filter_columns=filter_columns,
flierprops={
'markersize': 2,
'marker': 'o'
},
box_width=0.4,
box_spacing=0.2,
return_full_dataframes=False,
whis='range')
sns.despine(ax=fraction_licks_by_session_A_ax, top=True, right=True)
fraction_licks_by_session_A_ax.set_xticklabels(['first', 'last'])
fraction_licks_by_session_A_ax.set_xlabel('')
fraction_licks_by_session_A_ax.set_ylim(-0.02, 0.6)
fraction_licks_by_session_A_ax.set_yticks([0, 0.2, 0.4, 0.6])
fraction_licks_by_session_A_ax.set_title('')
fraction_licks_by_session_A_ax.legend(loc='upper left', fontsize=6)
# fraction_licks_by_session_A_ax.get_legend().set_visible(False)
fraction_licks_by_session_A_ax.text(
0.5,
.95,
r'$\mathrm{I}$',
ha='center',
va='center',
transform=fraction_licks_by_session_A_ax.transAxes,
fontsize=12)
filter_fn = lambda df: (df['X_session'] != '1') & (df['X_condition'] == 'B'
)
filter_columns = ['X_session', 'X_condition']
plot_metric(fraction_licks_by_session_B_ax,
expt_grps,
metric_fn=behavior_fn,
activity_kwargs=behavior_kwargs,
groupby=groupby,
plotby=plotby,
plot_method='box_and_line',
activity_label=activity_label,
colors=colors,
label_every_n=1,
label_groupby=False,
markers=markers,
rotate_labels=False,
line_kwargs=line_kwargs,
linestyles=linestyles,
filter_fn=filter_fn,
filter_columns=filter_columns,
notch=False,
flierprops={
'markersize': 2,
'marker': 'o'
},
box_width=0.4,
box_spacing=0.2,
return_full_dataframes=False,
whis='range')
sns.despine(ax=fraction_licks_by_session_B_ax,
top=True,
right=True,
left=True)
fraction_licks_by_session_B_ax.tick_params(left=False, labelleft=False)
fraction_licks_by_session_B_ax.set_xticklabels(['first', 'last'])
fraction_licks_by_session_B_ax.set_xlabel('Session in day')
fraction_licks_by_session_B_ax.set_ylabel('')
fraction_licks_by_session_B_ax.set_ylim(-0.02, 0.6)
fraction_licks_by_session_B_ax.set_title('')
fraction_licks_by_session_B_ax.get_legend().set_visible(False)
fraction_licks_by_session_B_ax.text(
0.5,
.95,
r'$\mathrm{II}$',
ha='center',
va='center',
transform=fraction_licks_by_session_B_ax.transAxes,
fontsize=12)
filter_fn = lambda df: (df['X_session'] != '1') & (df['X_condition'] == 'C'
)
filter_columns = ['X_session', 'X_condition']
plot_metric(fraction_licks_by_session_C_ax,
expt_grps,
metric_fn=behavior_fn,
activity_kwargs=behavior_kwargs,
groupby=groupby,
plotby=plotby,
plot_method='box_and_line',
activity_label=activity_label,
colors=colors,
notch=False,
label_every_n=1,
label_groupby=False,
markers=markers,
rotate_labels=False,
line_kwargs=line_kwargs,
linestyles=linestyles,
filter_fn=filter_fn,
filter_columns=filter_columns,
return_full_dataframes=False,
flierprops={
'markersize': 2,
'marker': 'o'
},
box_width=0.4,
box_spacing=0.2,
whis='range')
sns.despine(ax=fraction_licks_by_session_C_ax,
top=True,
right=True,
left=True)
fraction_licks_by_session_C_ax.tick_params(left=False, labelleft=False)
fraction_licks_by_session_C_ax.set_xticklabels(['first', 'last'])
fraction_licks_by_session_C_ax.set_xlabel('')
fraction_licks_by_session_C_ax.set_ylabel('')
fraction_licks_by_session_C_ax.set_ylim(-0.02, 0.6)
fraction_licks_by_session_C_ax.set_title('')
fraction_licks_by_session_C_ax.get_legend().set_visible(False)
fraction_licks_by_session_C_ax.text(
0.5,
.95,
r'$\mathrm{III}$',
ha='center',
va='center',
transform=fraction_licks_by_session_C_ax.transAxes,
fontsize=12)
misc.save_figure(fig, filename, save_dir=save_dir)
plt.close('all')
def main():
all_grps = df.loadExptGrps('GOL')
expt_grps = [all_grps['WT_place_set'], all_grps['Df_place_set']]
pc_filters = [expt_grp.pcs_filter(roi_filter=roi_filter) for
expt_grp, roi_filter in zip(expt_grps, roi_filters)]
fig = plt.figure(figsize=(8.5, 11))
gs1 = plt.GridSpec(
3, 3, left=0.1, right=0.9, top=0.9, bottom=0.3, wspace=0.5, hspace=0.4)
sensitivity_cdf_ax = fig.add_subplot(gs1[1, 0])
sensitivity_bar_ax = fig.add_axes([0.24, 0.535, 0.05, 0.07])
specificity_cdf_ax = fig.add_subplot(gs1[1, 1])
specificity_bar_ax = fig.add_axes([0.43, 0.60, 0.05, 0.07])
width_cdf_ax = fig.add_subplot(gs1[2, 0])
width_bar_ax = fig.add_axes([0.24, 0.315, 0.05, 0.07])
sparsity_cdf_ax = fig.add_subplot(gs1[2, 1])
sparsity_bar_ax = fig.add_axes([0.54, 0.315, 0.05, 0.07])
is_ever_pc_fraction_ax = fig.add_subplot(gs1[0, 0])
pc_fraction_ax = fig.add_subplot(gs1[0, 1])
pc_fraction_bar_ax = fig.add_axes([0.54, 0.755, 0.05, 0.07])
cdf_axs = [
sensitivity_cdf_ax, specificity_cdf_ax, width_cdf_ax, sparsity_cdf_ax,
pc_fraction_ax]
bar_axs = [
sensitivity_bar_ax, specificity_bar_ax, width_bar_ax, sparsity_bar_ax,
pc_fraction_bar_ax]
sensitivity_range = (0, 1)
plotting.plot_metric(
sensitivity_cdf_ax, expt_grps, metric_fn=place.sensitivity,
groupby=[['roi_id', 'expt']], plotby=None, plot_method='cdf',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Transient sensitivity', colors=colors,
rotate_labels=False, linestyles=linestyles)
sensitivity_cdf_ax.set_xlim(sensitivity_range)
plotting.plot_metric(
sensitivity_bar_ax, expt_grps, metric_fn=place.sensitivity,
groupby=[['roi_id', 'expt'],
['roi_id', 'uniqueLocationKey', 'mouseID'], ['mouseID']],
plotby=None, plot_method='grouped_bar',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Transient sensitivity', colors=colors)
sensitivity_bar_ax.set_ylim(sensitivity_range)
sensitivity_bar_ax.set_yticks(sensitivity_range)
plotting.stackedText(
sensitivity_cdf_ax, [WT_label, Df_label], colors=colors, loc=2,
size=10)
specificity_range = (0, 1)
plotting.plot_metric(
specificity_cdf_ax, expt_grps, metric_fn=place.specificity,
groupby=[['roi_id', 'expt']], plotby=None, plot_method='cdf',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Transient specificity', colors=colors,
rotate_labels=False, linestyles=linestyles)
specificity_cdf_ax.set_xlim(specificity_range)
plotting.plot_metric(
specificity_bar_ax, expt_grps, metric_fn=place.specificity,
groupby=[['roi_id', 'expt'],
['roi_id', 'uniqueLocationKey', 'mouseID'], ['mouseID']],
plotby=None, plot_method='grouped_bar',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Transient specificity', colors=colors)
specificity_bar_ax.set_ylim(specificity_range)
specificity_bar_ax.set_yticks(specificity_range)
width_range = (0, 100)
plotting.plot_metric(
width_cdf_ax, expt_grps, metric_fn=place.place_field_width,
groupby=None, plotby=None, plot_method='cdf',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Place field width (cm)', colors=colors,
rotate_labels=False, linestyles=linestyles)
width_cdf_ax.set_xlim(width_range)
plotting.plot_metric(
width_bar_ax, expt_grps, metric_fn=place.place_field_width,
groupby=[['roi_id', 'uniqueLocationKey', 'mouseID'], ['mouseID']],
plotby=None, plot_method='grouped_bar',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Place field width', colors=colors)
width_bar_ax.set_ylim(width_range)
width_bar_ax.set_yticks(width_range)
sparsity_range = (0, 1)
plotting.plot_metric(
sparsity_cdf_ax, expt_grps, metric_fn=place.sparsity,
groupby=[['roi_id', 'expt']], plotby=None, plot_method='cdf',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Single-cell sparsity', colors=colors,
rotate_labels=False, linestyles=linestyles)
sparsity_cdf_ax.set_xlim(sparsity_range)
plotting.plot_metric(
sparsity_bar_ax, expt_grps, metric_fn=place.sparsity,
groupby=[['roi_id', 'expt'],
['roi_id', 'uniqueLocationKey', 'mouseID'], ['mouseID']],
plotby=None, plot_method='grouped_bar',
roi_filters=pc_filters, activity_kwargs=None,
activity_label='Single-cell sparsity', colors=colors)
sparsity_bar_ax.set_ylim(sparsity_range)
sparsity_bar_ax.set_yticks(sparsity_range)
fraction_ses_pc_range = (0, 0.5)
plotting.plot_metric(
pc_fraction_ax, expt_grps, metric_fn=lab.ExperimentGroup.filtered_rois,
groupby=(('mouseID', 'uniqueLocationKey', 'roi_id'),), plotby=None,
colorby=None, plot_method='cdf', roi_filters=pc_filters,
activity_kwargs=[
{'include_roi_filter': roi_filter} for roi_filter in roi_filters],
colors=colors, activity_label='Fraction of sessions a place cell',
rotate_labels=False, linestyles=linestyles)
pc_fraction_ax.tick_params(length=3, pad=2)
pc_fraction_ax.get_legend().set_visible(False)
pc_fraction_ax.set_title('')
pc_fraction_ax.set_xticks([0, .2, .4, .6, .8])
pc_fraction_ax.set_xlim(0, .8)
pc_fraction_ax.spines['left'].set_linewidth(1)
pc_fraction_ax.spines['bottom'].set_linewidth(1)
plotting.plot_metric(
pc_fraction_bar_ax, expt_grps,
metric_fn=lab.ExperimentGroup.filtered_rois,
groupby=[['roi_id', 'uniqueLocationKey', 'mouseID'], ['mouseID']],
plotby=None, plot_method='grouped_bar',
roi_filters=pc_filters, activity_kwargs=[
{'include_roi_filter': roi_filter} for roi_filter in roi_filters],
activity_label='Fraction of sessions a place cell', colors=colors)
pc_fraction_bar_ax.set_ylim(fraction_ses_pc_range)
pc_fraction_bar_ax.set_yticks(fraction_ses_pc_range)
place.is_ever_place_cell(
expt_grps, roi_filters=roi_filters, ax=is_ever_pc_fraction_ax,
colors=colors, filter_fn=lambda df: df['session_number'] < 15,
filter_columns=['session_number'],
groupby=[['mouseID', 'session_number']])
is_ever_pc_fraction_ax.get_legend().set_visible(False)
is_ever_pc_fraction_ax.tick_params(length=3, pad=2)
is_ever_pc_fraction_ax.set_xlabel('Session number')
is_ever_pc_fraction_ax.set_title('Lifetime place coding')
is_ever_pc_fraction_ax.set_xticklabels([
'1', '', '3', '', '5', '', '7', '', '9', '', '11', '', '13', '', '15'])
for ax in cdf_axs + bar_axs:
ax.tick_params(length=3, pad=2)
for ax in cdf_axs:
ax.set_title('')
for ax in bar_axs:
ax.set_xlabel('')
ax.set_ylabel('')
ax.set_title('')
ax.set_xticks([])
ax.tick_params(bottom=False, labelbottom=False, length=3, pad=2)
ax.get_legend().set_visible(False)
sns.despine(fig)
misc.save_figure(fig, filename, save_dir=save_dir)
plt.close('all')
