Explained Variance¶
Setup¶
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%reload_ext autoreload
%autoreload 2
import matplotlib.pyplot as plt
import nelpy as nel
from neuro_py.ensemble.explained_variance import ExplainedVariance
from neuro_py.io import loading
from neuro_py.plotting.events import plot_peth_fast
from neuro_py.plotting.figure_helpers import set_plotting_defaults
set_plotting_defaults()
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
fig_save_path = r"Z:\home\ryanh\projects\hpc_ctx\figures\panels"
%reload_ext autoreload %autoreload 2 import matplotlib.pyplot as plt import nelpy as nel from neuro_py.ensemble.explained_variance import ExplainedVariance from neuro_py.io import loading from neuro_py.plotting.events import plot_peth_fast from neuro_py.plotting.figure_helpers import set_plotting_defaults set_plotting_defaults() %matplotlib inline %config InlineBackend.figure_format = 'retina' fig_save_path = r"Z:\home\ryanh\projects\hpc_ctx\figures\panels"
Section 1: Load spike data, session epochs, and Non-REM epochs¶
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basepath = r"U:\data\HMC\HMC1\day8"
st, cm = loading.load_spikes(basepath, brainRegion="CA1", putativeCellType="Pyr")
epoch_df = loading.load_epoch(basepath)
beh_epochs = nel.EpochArray(epoch_df[["startTime", "stopTime"]].values)
state_dict = loading.load_SleepState_states(basepath)
nrem_epochs = nel.EpochArray(
state_dict["NREMstate"],
)
epoch_df
basepath = r"U:\data\HMC\HMC1\day8" st, cm = loading.load_spikes(basepath, brainRegion="CA1", putativeCellType="Pyr") epoch_df = loading.load_epoch(basepath) beh_epochs = nel.EpochArray(epoch_df[["startTime", "stopTime"]].values) state_dict = loading.load_SleepState_states(basepath) nrem_epochs = nel.EpochArray( state_dict["NREMstate"], ) epoch_df
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| name | startTime | stopTime | environment | behavioralParadigm | notes | manipulation | stimuli | basepath | |
|---|---|---|---|---|---|---|---|---|---|
| 0 | preSleep_210411_064951 | 0.0000 | 9544.56315 | sleep | NaN | NaN | NaN | NaN | U:\data\HMC\HMC1\day8 |
| 1 | maze_210411_095201 | 9544.5632 | 11752.80635 | linear | 1 | novel | NaN | NaN | U:\data\HMC\HMC1\day8 |
| 2 | postSleep_210411_103522 | 11752.8064 | 23817.68955 | sleep | NaN | NaN | NaN | NaN | U:\data\HMC\HMC1\day8 |
Section 2: Single output metrics: Explained and Reverse Explained Variance¶
Here we are calculating explained variance over the entire post-task interval
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ev = ExplainedVariance(
st=st,
template=beh_epochs[1], # task
matching=beh_epochs[2], # post sleep
control=beh_epochs[0], # pre sleep
window=None, # window size to calculate correlations, None is the full epoch
)
print(f"explained variance: {ev.ev[0]}, reverse explained variance: {ev.rev[0]}")
ev = ExplainedVariance( st=st, template=beh_epochs[1], # task matching=beh_epochs[2], # post sleep control=beh_epochs[0], # pre sleep window=None, # window size to calculate correlations, None is the full epoch ) print(f"explained variance: {ev.ev[0]}, reverse explained variance: {ev.rev[0]}")
WARNING:root:ignoring events outside of eventarray support
explained variance: 0.10214717079493098, reverse explained variance: 0.002093670634183538
You can calculate a p-value for the explained variance by comparing the explained variance to the explained variance of shuffled data (shuffled template correlations).
NOTE: This only works when returning single explained variance value, not a set of explained variance values over time.
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pvalue = ev.pvalue()
print(f"pvalue: {pvalue}")
pvalue = ev.pvalue() print(f"pvalue: {pvalue}")
pvalue: 0.000999000999000999
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ev = ExplainedVariance(
st=st,
template=beh_epochs[1], # task
matching=beh_epochs, # entire epoch (uses start,stop)
control=beh_epochs[0], # pre sleep
window=200,
)
# conviently plot the explained variance with built in method
ev.plot()
ev = ExplainedVariance( st=st, template=beh_epochs[1], # task matching=beh_epochs, # entire epoch (uses start,stop) control=beh_epochs[0], # pre sleep window=200, ) # conviently plot the explained variance with built in method ev.plot()
WARNING:root:ignoring events outside of eventarray support
Section 3.2: Inspect when the explained variance is high and low¶
You can see it is high during the task (by definition it should be) and during NREM sleep
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plt.figure(figsize=(8, 3))
ax = plt.gca()
plot_peth_fast(ev.partial_corr.T, ts=ev.matching_time, ax=ax, label="EV")
plot_peth_fast(
ev.rev_partial_corr.T, ts=ev.matching_time, ax=ax, color="grey", label="REV"
)
plt.axvspan(
nrem_epochs.data[0, 0],
nrem_epochs.data[0, 1],
color="purple",
alpha=0.5,
label="NREM",
)
for nrem in nrem_epochs.data:
plt.axvspan(nrem[0], nrem[1], color="purple", alpha=0.5)
plt.axvspan(
beh_epochs[1].data[0, 0],
beh_epochs[1].data[0, 1],
color="b",
alpha=0.25,
zorder=-100,
label="Task",
)
plt.legend()
plt.show()
plt.figure(figsize=(8, 3)) ax = plt.gca() plot_peth_fast(ev.partial_corr.T, ts=ev.matching_time, ax=ax, label="EV") plot_peth_fast( ev.rev_partial_corr.T, ts=ev.matching_time, ax=ax, color="grey", label="REV" ) plt.axvspan( nrem_epochs.data[0, 0], nrem_epochs.data[0, 1], color="purple", alpha=0.5, label="NREM", ) for nrem in nrem_epochs.data: plt.axvspan(nrem[0], nrem[1], color="purple", alpha=0.5) plt.axvspan( beh_epochs[1].data[0, 0], beh_epochs[1].data[0, 1], color="b", alpha=0.25, zorder=-100, label="Task", ) plt.legend() plt.show()
Section 3.3: Use EpochArray to get average explained variance in post-task NREM sleep¶
The outcome is similar to above when we used the entire post-task epoch
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nrem_ev_avg = ev.ev_signal[beh_epochs[2] & nrem_epochs].mean()
nrem_rev_avg = ev.rev_signal[beh_epochs[2] & nrem_epochs].mean()
print(f"explained variance: {nrem_ev_avg}, reverse explained variance: {nrem_rev_avg}")
nrem_ev_avg = ev.ev_signal[beh_epochs[2] & nrem_epochs].mean() nrem_rev_avg = ev.rev_signal[beh_epochs[2] & nrem_epochs].mean() print(f"explained variance: {nrem_ev_avg}, reverse explained variance: {nrem_rev_avg}")
WARNING:root:ignoring signal outside of support WARNING:root:ignoring signal outside of support
explained variance: 0.10133556865860369, reverse explained variance: 0.001632476383922529