rz_end = saraharray[0, 12] trialno = np.max( saraharray[:, 9] ) # total number of trials for that day and mouse (used later for defining y axis max) # Extract data for beaconed, non-beaconed, probe dailymouse_b = np.delete(saraharray, np.where(saraharray[:, 8] > 0), 0) # delete all data not on beaconed tracks dailymouse_nb = np.delete(saraharray, np.where(saraharray[:, 8] != 10), 0) # delete all data not on non beaconed tracks dailymouse_p = np.delete(saraharray, np.where(saraharray[:, 8] != 20), 0) # delete all data not on probe tracks # extract stops stopsdata_b = extractstops_HUMAN(dailymouse_b) stopsdata_nb = extractstops_HUMAN(dailymouse_nb) stopsdata_p = extractstops_HUMAN(dailymouse_p) # get location and trial number of rewards reward_beac = extractrewards(dailymouse_b) reward_nbeac = extractrewards(dailymouse_nb) # filter stops (removes stops 0.5 cm after a stop) stopsdata_b = filterstops(stopsdata_b) stopsdata_nb = filterstops(stopsdata_nb) stopsdata_p = filterstops(stopsdata_p) # extract trial numbers from data (only unique ones) trialids_b = np.unique(stopsdata_b[:, 2]) trialids_nb = np.unique(stopsdata_nb[:, 2])
def plot_fig1F(session_paths, save_path): # specify mouse/mice and day/s to analyse days = [1] n_bins = 20 # specify mouse/mice and day/s to analyse days = ['Day' + str(int(x)) for x in np.arange(1)] # empty arrays for storing data firststopstorebeac = np.zeros((len(days), len(session_paths), n_bins, 2)) firststopstorenbeac = np.zeros((len(days), len(session_paths), n_bins, 2)) firststopstoreprobe = np.zeros((len(days), len(session_paths), n_bins, 2)) firststopstorebeac[:,:,:] = np.nan firststopstorenbeac[:,:,:] = np.nan firststopstoreprobe[:,:,:] = np.nan #loop days and mice to collect data for dcount,day in enumerate(days): session_count = 0 for session_path in session_paths: saraharray, track_start, track_end = translate_to_legacy_format(session_path) rz_start = saraharray[0, 11] rz_end = saraharray[0, 12] trialarray = maketrialarray(saraharray) # make array of trial number same size as saraharray saraharray[:,9] = trialarray[:,0] # replace trial number because of increment error (see README.py) # split data by trial type dailymouse_b = np.delete(saraharray, np.where(saraharray[:, 8] > 0), 0) # delete all data not on beaconed tracks dailymouse_nb = np.delete(saraharray, np.where(saraharray[:, 8] != 10), 0)# delete all data not on non beaconed tracks dailymouse_p = np.delete(saraharray, np.where(saraharray[:, 8] != 20), 0)# delete all data not on probe tracks #extract stops stopsdata_b = extractstops_HUMAN(dailymouse_b) stopsdata_nb = extractstops_HUMAN(dailymouse_nb) stopsdata_p = extractstops_HUMAN(dailymouse_p) # filter stops stopsdata_b = filterstops(stopsdata_b) stopsdata_nb = filterstops(stopsdata_nb) stopsdata_p = filterstops(stopsdata_p) trialids_b = np.unique(stopsdata_b[:, 2]) # make array of unique trial numbers srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stopsdata_b,trialids_b) # get average real stops & shuffled stops per lcoation bin zscore_b = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) # calculate z-scores firststopstorebeac[dcount, session_count,:,1] = zscore_b # store zscores if stopsdata_nb.size > 0: # if there is non-beaconed data trialids_nb = np.unique(stopsdata_nb[:, 2]) # make array of unique trial numbers srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stopsdata_nb, trialids_nb) # get average real stops & shuffled stops per lcoation bin zscore_nb = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) # calculate z-scores firststopstorenbeac[dcount, session_count,:,1] = zscore_nb # store zscores if stopsdata_p.size > 0: # if there is probe data trialids_p = np.unique(stopsdata_p[:, 2]) # make array of unique trial numbers srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stopsdata_p, trialids_p) # get average real stops & shuffled stops per lcoation bin zscore_p = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) # calculate z-scores firststopstoreprobe[dcount, session_count,:,1] = zscore_p # store zscores session_count += 1 # AVERAGE DATA FOR PLOTS # stack experiments then average over days then mice con_b1 = np.nanmean(((firststopstorebeac[0, :, :,1])), axis=0) con_nb1 = np.nanmean(((firststopstorenbeac[0, :, :,1])), axis=0) con_p1 = np.nanmean(((firststopstoreprobe[0,:, :, 1])), axis=0) sdcon_b1 = np.nanstd(((firststopstorebeac[0, :, :,1])), axis=0)/math.sqrt(session_count) sdcon_nb1 = np.nanstd(((firststopstorenbeac[0, :, :,1])), axis=0)/ math.sqrt(session_count) sdcon_p1 = np.nanstd(((firststopstoreprobe[0, :, :,1])), axis=0)/ math.sqrt(session_count) # PLOT GRAPHS bins = np.arange(0.5,n_bins+0.5,1) # track bins fig = plt.figure(figsize = (12,4)) ax = fig.add_subplot(1,3,1) ax.set_title('Beaconed', fontsize=20, verticalalignment='bottom', style='italic') # title ax.axvspan(rz_start, rz_end, facecolor='g', alpha=0.25, hatch = '/', linewidth =0) # green box spanning the rewardzone - to mark reward zone ax.axvspan(0, track_start, facecolor='k', alpha=0.15, hatch = '/', linewidth =0) # black box ax.axvspan(track_end, 20, facecolor='k', alpha=0.15, hatch = '/', linewidth =0)# black box ax.axvline(0, linewidth = 3, color = 'black') # bold line on the y axis ax.axhline(-10, linewidth = 3, color = 'black') # bold line on the x axis ax.axhline(0, linewidth = 1,ls='--', color = 'black') # bold line on the x axis #ax.plot(bins*5,con_b,color = 'red',label = 'AAV-fl-GFP', linewidth = 2) #plot becaoned trials #ax.fill_between(bins*5,con_b-sdcon_b,con_b+sdcon_b, facecolor = 'red', alpha = 0.3) ax.plot(bins,con_b1,'',color = 'blue',label = 'AAV-fl-GFP', linewidth = 2) #plot becaoned trials ax.fill_between(bins,con_b1-sdcon_b1,con_b1+sdcon_b1, facecolor = 'blue', alpha = 0.3) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.set_xlim(0,20) ax.set_ylim(-10,35) adjust_spines(ax, ['left','bottom']) # removes top and right spines ax.locator_params(axis = 'x', nbins=3) # set number of ticks on x axis ax.locator_params(axis = 'y', nbins=5) # set number of ticks on y axis ax.set_xticklabels(['0', '10', '20']) ax.set_yticklabels(['-10','0','10','20', '30']) ax = plt.ylabel('Stops (Zscore)', fontsize=16, labelpad = 18) ax = fig.add_subplot(1,3,2) #stops per trial ax.set_title('Non-Beaconed', fontsize=20, verticalalignment='bottom', style='italic') # title ax.axvspan(rz_start, rz_end, facecolor='g', alpha=0.25, hatch = '/', linewidth =0) # green box spanning the rewardzone - to mark reward zone ax.axvspan(0, track_start, facecolor='k', alpha=0.15, hatch = '/', linewidth =0) # black box ax.axvspan(track_end, 20, facecolor='k', alpha=0.15, hatch = '/', linewidth =0)# black box ax.axvline(0, linewidth = 3, color = 'black') # bold line on the y axis ax.axhline(-10, linewidth = 3, color = 'black') # bold line on the x axis ax.axhline(0, linewidth = 1,ls='--', color = 'black') # bold line on the x axis #ax.plot(bins*5,con_nb,color = 'red', linewidth = 2) #plot becaoned trials #ax.fill_between(bins*5,con_nb-sdcon_nb,con_nb+sdcon_nb, facecolor = 'red', alpha = 0.3) ax.plot(bins,con_nb1,color = 'blue', linewidth = 2) #plot becaoned trials ax.fill_between(bins,con_nb1-sdcon_nb1,con_nb1+sdcon_nb1, facecolor = 'blue', alpha = 0.3) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.set_xlim(0,20) ax.set_ylim(-10,35) adjust_spines(ax, ['left','bottom']) # re;moves top and right spines ax.locator_params(axis = 'x', nbins=3) # set number of ticks on x axis ax.locator_params(axis = 'y', nbins=5) # set number of ticks on y axis ax.set_xticklabels(['0', '10', '20']) ax.set_yticklabels(['','','','', '']) ax = plt.xlabel('Location (VU)', fontsize=16, labelpad = 18) ax = fig.add_subplot(1,3,3) #stops per trial ax.set_title('Probe', fontsize=20, verticalalignment='bottom', style='italic') # title ax.axvspan(rz_start, rz_end, facecolor='g', alpha=0.25, hatch = '/', linewidth =0) # green box spanning the rewardzone - to mark reward zone ax.axvspan(0, track_start, facecolor='k', alpha=0.15, hatch = '/', linewidth =0) # black box ax.axvspan(track_end, 20, facecolor='k', alpha=0.15, hatch = '/', linewidth =0)# black box ax.axhline(0, linewidth = 1,ls='--', color = 'black') # bold line on the x axis ax.axvline(0, linewidth = 3, color = 'black') # bold line on the y axis ax.axhline(-10, linewidth = 3, color = 'black') # bold line on the x axis #ax.plot(bins*5,con_p,color = 'red', label = 'Beaconed', linewidth = 2) #plot becaoned trials #ax.fill_between(bins*5,con_p-sdcon_p,con_p+sdcon_p, facecolor = 'red', alpha = 0.3) ax.plot(bins,con_p1,color = 'blue', label = 'Beaconed', linewidth = 2) #plot becaoned trials ax.fill_between(bins,con_p1-sdcon_p1,con_p1+sdcon_p1, facecolor = 'blue', alpha = 0.3) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.set_xlim(0,20) ax.set_ylim(-10,35) adjust_spines(ax, ['left','bottom']) # removes top and right spines ax.locator_params(axis = 'x', nbins=3) # set number of ticks on x axis ax.locator_params(axis = 'y', nbins=5) # set number of ticks on y axis ax.set_xticklabels(['0', '10', '20']) ax.set_yticklabels(['','','','', '']) plt.subplots_adjust(hspace = .35, wspace = .35, bottom = 0.25, left = 0.15, right = 0.82, top = 0.85) fig.savefig(save_path, dpi=200) plt.close()
def plot_fig1D(session_paths, save_path): days = [1] n_bins = 20 # specify mouse/mice and day/s to analyse days = ['Day' + str(int(x)) for x in np.arange(1)] # Arrays for storing data (output) firststopstorebeac = np.zeros((len(days), len(session_paths), n_bins, 2)) firststopstorenbeac = np.zeros((len(days), len(session_paths), n_bins, 2)) firststopstoreprobe = np.zeros((len(days), len(session_paths), n_bins, 2)) firststopstorebeac[:, :, :, :] = np.nan firststopstorenbeac[:, :, :, :] = np.nan firststopstoreprobe[:, :, :, :] = np.nan # For each day and mouse, pull raw data, calculate first stops and store data for dcount, day in enumerate(days): session_count = 0 for session_path in session_paths: saraharray, track_start, track_end = translate_to_legacy_format( session_path) rz_start = saraharray[0, 11] rz_end = saraharray[0, 12] # make array of trial number for each row in dataset trialarray = maketrialarray( saraharray) # write array of trial per row in datafile saraharray[:, 9] = trialarray[:, 0] # replace trial column in dataset *see README for why this is done* # split data by trial type dailymouse_b = np.delete(saraharray, np.where(saraharray[:, 8] > 0), 0) dailymouse_nb = np.delete(saraharray, np.where(saraharray[:, 8] != 10), 0) dailymouse_p = np.delete(saraharray, np.where(saraharray[:, 8] != 20), 0) # get stops stops_b = extractstops_HUMAN(dailymouse_b) stops_nb = extractstops_HUMAN(dailymouse_nb) stops_p = extractstops_HUMAN(dailymouse_p) #filterstops stops_b = filterstops(stops_b) stops_nb = filterstops(stops_nb) stops_p = filterstops(stops_p) # get first stop for each trial trarray = np.arange(np.min(saraharray[:, 9]), np.max(saraharray[:, 9] + 0.1), 1) # array of trial numbers beac = [] nbeac = [] probe = [] # make empty arrays to store data trialids_b = np.unique(stops_b[:, 2]) # find unique trial numbers stops_f_b = FirstStops_humans( trarray, stops_b, track_start, track_end) # get locations of first stop for each trial stops_f_b = create_srdata(stops_f_b, trialids_b) # bin first stop data beac = np.nanmean( stops_f_b, axis=0) # average times mouse stops first in each bin if stops_nb.size > 0: trialids_nb = np.unique(stops_nb[:, 2]) stops_f_nb = FirstStops_humans( trarray, stops_nb, track_start, track_end) # get locations of first stop for each trial stops_f_nb = create_srdata(stops_f_nb, trialids_nb) # bin first stop data nbeac = np.nanmean( stops_f_nb, axis=0) # average times mouse stops first in each bin if stops_p.size > 0: trialids_p = np.unique(stops_p[:, 2]) stops_f_p = FirstStops_humans( trarray, stops_p, track_start, track_end) # get locations of first stop for each trial stops_f_p = create_srdata(stops_f_p, trialids_p) # bin first stop data probe = np.nanmean( stops_f_p, axis=0) # average times mouse stops first in each bin # store data #if mcount == 3 or mcount == 5 or mcount == 6 or mcount == 7 or mcount == 8: firststopstorebeac[dcount, session_count, :, 0] = beac # store first stop data srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3( stops_b, trialids_b) # get average stops per location bin firststopstorebeac[dcount, session_count, :, 1] = srbin_mean # store stops data if stops_nb.size > 0: firststopstorenbeac[dcount, session_count, :, 0] = nbeac # store first stop data srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3( stops_nb, trialids_nb) # get average stops per location bin firststopstorenbeac[dcount, session_count, :, 1] = srbin_mean # store stops data if stops_p.size > 0: firststopstoreprobe[dcount, session_count, :, 0] = probe # store first stop data srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3( stops_p, trialids_p) # get average stops per location bin firststopstoreprobe[dcount, session_count, :, 1] = srbin_mean # store stops data session_count += 1 # Average over days for all mice # week 1 (first stop) con_beac_w1 = np.nanmean(((firststopstorebeac[0, :, :, 0])), axis=0) con_nbeac_w1 = np.nanmean(((firststopstorenbeac[0, :, :, 0])), axis=0) con_probe_w1 = np.nanmean(((firststopstoreprobe[0, :, :, 0])), axis=0) sd_con_beac_w1 = np.nanstd( ((firststopstorebeac[0, :, :, 0])), axis=0) / math.sqrt(session_count) sd_con_nbeac_w1 = np.nanstd( ((firststopstorenbeac[0, :, :, 0])), axis=0) / math.sqrt(session_count) sd_con_probe_w1 = np.nanstd( ((firststopstoreprobe[0, :, :, 0])), axis=0) / math.sqrt(session_count) # week 1 (all stops) con_beac1_w1 = np.nanmean(((firststopstorebeac[0, :, :, 1])), axis=0) con_nbeac1_w1 = np.nanmean(((firststopstorenbeac[0, :, :, 1])), axis=0) con_probe1_w1 = np.nanmean(((firststopstoreprobe[0, :, :, 1])), axis=0) sd_con_beac1_w1 = np.nanstd( ((firststopstorebeac[0, :, :, 1])), axis=0) / math.sqrt(session_count) sd_con_nbeac1_w1 = np.nanstd( ((firststopstorenbeac[0, :, :, 1])), axis=0) / math.sqrt(session_count) sd_con_probe1_w1 = np.nanstd( ((firststopstoreprobe[0, :, :, 1])), axis=0) / math.sqrt(session_count) ''' # week 4 (first stop) con_beac_w4 = np.nanmean(np.nanmean(((firststopstorebeac[18:22,:,:,0])), axis = 0), axis = 0) con_nbeac_w4 = np.nanmean(np.nanmean(((firststopstorenbeac[18:22,:,:,0])), axis =0), axis = 0) con_probe_w4 = np.nanmean(np.nanmean(((firststopstoreprobe[18:22,:,:,0])), axis = 0), axis = 0) sd_con_beac_w4 = np.nanstd(np.nanmean(((firststopstorebeac[18:22,:,:,0])), axis = 0), axis = 0)/math.sqrt(8) sd_con_nbeac_w4 = np.nanstd(np.nanmean(((firststopstorenbeac[18:22,:,:,0])), axis =0), axis = 0)/math.sqrt(8) sd_con_probe_w4 = np.nanstd(np.nanmean(((firststopstoreprobe[18:22,:,:,0])), axis = 0), axis = 0)/math.sqrt(8) # week 4 (all stops) con_beac1_w4 = np.nanmean(np.nanmean(((firststopstorebeac[18:22,:,:,1])), axis = 0), axis = 0) con_nbeac1_w4 = np.nanmean(np.nanmean(((firststopstorenbeac[18:22,:,:,1])), axis =0), axis = 0) con_probe1_w4 = np.nanmean(np.nanmean(((firststopstoreprobe[18:22,:,:,1])), axis = 0), axis = 0) sd_con_beac1_w4 = np.nanstd(np.nanmean(((firststopstorebeac[18:22,:,:,1])), axis = 0), axis = 0)/math.sqrt(8) sd_con_nbeac1_w4 = np.nanstd(np.nanmean(((firststopstorenbeac[18:22,:,:,1])), axis =0), axis = 0)/math.sqrt(8) sd_con_probe1_w4 = np.nanstd(np.nanmean(((firststopstoreprobe[18:22,:,:,1])), axis = 0), axis = 0)/math.sqrt(8) ''' # PLOT GRAPHS bins = np.arange(0.5, n_bins + 0.5, 1) # first stop histogram fig = plt.figure(figsize=(12, 4)) ax = fig.add_subplot(1, 3, 1) #stops per trial ax.set_title('Beaconed', fontsize=20, verticalalignment='bottom', style='italic') # title ax.axvspan( rz_start, rz_end, facecolor='g', alpha=0.25, hatch='/', linewidth=0) # green box spanning the rewardzone - to mark reward zone ax.axvspan(0, track_start, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box ax.axvspan(track_end, 20, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box ax.axvline(0, linewidth=3, color='black') # bold line on the y axis ax.axhline(0, linewidth=3, color='black') # bold line on the x axis ax.plot(bins, con_beac_w1, color='blue', label='Beaconed', linewidth=2) #plot becaoned trials ax.fill_between(bins, con_beac_w1 - sd_con_beac_w1, con_beac_w1 + sd_con_beac_w1, facecolor='blue', alpha=0.3) #ax.plot(bins,con_beac_w4,color = 'red',label = 'Beaconed', linewidth = 2) #plot becaoned trials #ax.fill_between(bins,con_beac_w4-sd_con_beac_w4,con_beac_w4+sd_con_beac_w4, facecolor = 'red', alpha = 0.3) ax.tick_params(axis='x', pad=10, top='off', right='off', direction='out', width=2, length=7, labelsize=16) ax.tick_params(axis='y', pad=10, top='off', right='off', direction='out', width=2, length=7, labelsize=16) ax.set_xlim(0, 20) ax.set_ylim(0, 0.95) adjust_spines(ax, ['left', 'bottom']) # removes top and right spines ax.locator_params(axis='x', nbins=3) # set number of ticks on x axis ax.locator_params(axis='y', nbins=4) # set number of ticks on y axis ax.set_xticklabels(['0', '10', '20']) ax.set_yticklabels(['0', '0.3', '0.6', '0.9']) ax.set_ylabel('1st stop probability', fontsize=16, labelpad=18) ax = fig.add_subplot(1, 3, 2) #stops per trial ax.set_title('Non-Beaconed', fontsize=20, verticalalignment='bottom', style='italic') # title ax.axvspan( rz_start, rz_end, facecolor='g', alpha=0.25, hatch='/', linewidth=0) # green box spanning the rewardzone - to mark reward zone ax.axvspan(0, track_start, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box ax.axvspan(track_end, 20, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box ax.axvline(0, linewidth=3, color='black') # bold line on the y axis ax.axhline(0, linewidth=3, color='black') # bold line on the x axis ax.plot(bins, con_nbeac_w1, color='blue', linewidth=2) #plot becaoned trials ax.fill_between(bins, con_nbeac_w1 - sd_con_nbeac_w1, con_nbeac_w1 + sd_con_nbeac_w1, facecolor='blue', alpha=0.3) #ax.plot(bins,con_nbeac_w4,color = 'red', linewidth = 2) #plot becaoned trials #ax.fill_between(bins,con_nbeac_w4-sd_con_nbeac_w4,con_nbeac_w4+sd_con_nbeac_w4, facecolor = 'red', alpha = 0.3) ax.tick_params(axis='x', pad=10, top='off', right='off', direction='out', width=2, length=7, labelsize=16) ax.tick_params(axis='y', pad=10, top='off', right='off', direction='out', width=2, length=7, labelsize=16) ax.set_xlim(0, 20) ax.set_ylim(0, 0.95) adjust_spines(ax, ['left', 'bottom']) # re;moves top and right spines ax.locator_params(axis='x', nbins=3) # set number of ticks on x axis ax.locator_params(axis='y', nbins=4) # set number of ticks on y axis ax.set_xticklabels(['0', '10', '20']) ax.set_yticklabels(['', '', '', '']) ax.set_xlabel('Distance (VU)', fontsize=16, labelpad=18) ax = fig.add_subplot(1, 3, 3) #stops per trial ax.set_title('Probe', fontsize=20, verticalalignment='bottom', style='italic') # title ax.axvspan( rz_start, rz_end, facecolor='g', alpha=0.25, hatch='/', linewidth=0) # green box spanning the rewardzone - to mark reward zone ax.axvspan(0, track_start, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box ax.axvspan(track_end, 20, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box ax.axvline(0, linewidth=3, color='black') # bold line on the y axis ax.axhline(0, linewidth=3, color='black') # bold line on the x axis ax.plot(bins, con_probe_w1, color='blue', label='Beaconed', linewidth=2) #plot becaoned trials ax.fill_between(bins, con_probe_w1 - sd_con_probe_w1, con_probe_w1 + sd_con_probe_w1, facecolor='blue', alpha=0.3) #ax.plot(bins,con_probe_w4,color = 'red', label = 'Beaconed', linewidth = 2) #plot becaoned trials #ax.fill_between(bins,con_probe_w4-sd_con_probe_w4,con_probe_w4+sd_con_probe_w4, facecolor = 'red', alpha = 0.3) ax.tick_params(axis='x', pad=10, top='off', right='off', direction='out', width=2, length=7, labelsize=16) ax.tick_params(axis='y', pad=10, top='off', right='off', direction='out', width=2, length=7, labelsize=16) ax.set_xlim(0, 20) ax.set_ylim(0, 0.95) adjust_spines(ax, ['left', 'bottom']) # removes top and right spines ax.locator_params(axis='x', nbins=3) # set number of ticks on x axis ax.locator_params(axis='y', nbins=4) # set number of ticks on y axis ax.set_yticklabels(['', '', '', '']) ax.set_xticklabels(['0', '10', '20']) plt.subplots_adjust(hspace=.35, wspace=.35, bottom=0.25, left=0.15, right=0.82, top=0.85) fig.savefig(save_path, dpi=200) plt.close()
def plot_fig1E(session_paths, save_path): days = [1] # specify mouse/mice and day/s to analyse # choose specific day/s number_of_trials = 1000 # arbitrarily large amount of trials so we can catch all the trials # Arrays for storing data (output) firststopstorebeac = np.zeros(((number_of_trials), len(session_paths))) firststopstorenbeac = np.zeros(((number_of_trials), len(session_paths))) firststopstoreprobe = np.zeros(((number_of_trials), len(session_paths))) firststopstorebeac[:,:] = np.nan firststopstorenbeac[:,:] = np.nan firststopstoreprobe[:,:] = np.nan sd_con_FirstStopsstorebeac = np.zeros(((number_of_trials), len(session_paths))) sd_con_FirstStopsstorenbeac = np.zeros(((number_of_trials), len(session_paths))) sd_con_FirstStopsstoreprobe = np.zeros(((number_of_trials), len(session_paths))) sd_con_FirstStopsstorebeac[:, :] = np.nan sd_con_FirstStopsstorenbeac[:, :] = np.nan sd_con_FirstStopsstoreprobe[:, :] = np.nan # For each day and mouse, pull raw data, calculate first stops and store data for dcount,day in enumerate(days): session_count = 0 for session_path in session_paths: saraharray, track_start, track_end = translate_to_legacy_format(session_path) rz_start = saraharray[0, 11] rz_end = saraharray[0, 12] # make array of trial number for each row in dataset trialarray = maketrialarray(saraharray) # write array of trial per row in datafile saraharray[:,9] = trialarray[:,0] # replace trial column in dataset *see README for why this is done* # split data by trial type dailymouse_b = np.delete(saraharray, np.where(saraharray[:, 8] > 0), 0) dailymouse_nb = np.delete(saraharray, np.where(saraharray[:, 8] != 10), 0) dailymouse_p = np.delete(saraharray, np.where(saraharray[:, 8] != 20), 0) # get stops stops_b = extractstops_HUMAN(dailymouse_b) stops_nb = extractstops_HUMAN(dailymouse_nb) stops_p= extractstops_HUMAN(dailymouse_p) #filterstops stops_b = filterstops(stops_b) stops_nb = filterstops(stops_nb) stops_p = filterstops(stops_p) # get first stop for each trial trarray = np.unique(trialarray[:, 0]) # get unique trial numbers stops_f_b = FirstStops_humans(trarray, stops_b, track_start, track_end) # get locations of first stop for each trial #beac = np.nanmean(stops_f_b, axis=0) # find average first stop location #sdbeac = np.nanstd(stops_f_b, axis=0) # get sd of first stop location if stops_nb.size > 0: stops_f_nb = FirstStops_humans(trarray, stops_nb, track_start, track_end) # get locations of first stop for each trial #nbeac = np.nanmean(stops_f_nb, axis=0) # find average first stop location #sdnbeac = np.nanstd(stops_f_nb, axis=0) # get sd of first stop location if stops_p.size > 0: stops_f_p = FirstStops_humans(trarray, stops_p, track_start, track_end) # get locations of first stop for each trial #probe = np.nanmean(stops_f_p, axis=0) # find average first stop location #sdprobe = np.nanstd(stops_f_p, axis=0) # get sd of first stop location for i in range(len(stops_f_b)): firststopstorebeac[i, session_count] = stops_f_b[i][0] #sd_con_FirstStopsstorebeac[dcount, session_count] = beac[0] if stops_nb.size > 0: for i in range(len(stops_f_nb)): firststopstorenbeac[i, session_count] = stops_f_nb[i][0] #sd_con_FirstStopsstorenbeac[dcount, session_count] = nbeac[0] if stops_p.size > 0: for i in range(len(stops_f_p)): firststopstoreprobe[i, session_count] = stops_f_p[i][0] #sd_con_FirstStopsstoreprobe[dcount, session_count] = probe[0] session_count += 1 # Average over days for all mice con_beac = np.nanmean(((firststopstorebeac)), axis=1) con_beac = con_beac[~np.isnan(con_beac)] con_nbeac = np.nanmean(((firststopstorenbeac)), axis=1) con_nbeac = con_nbeac[~np.isnan(con_nbeac)] con_probe = np.nanmean(((firststopstoreprobe)), axis=1) con_probe = con_probe[~np.isnan(con_probe)] sd_con_beac = np.nanstd(((firststopstorebeac)), axis=1) / math.sqrt(session_count) sd_con_beac = sd_con_beac[~np.isnan(sd_con_beac)] sd_con_nbeac = np.nanstd(((firststopstorenbeac)), axis=1) / math.sqrt(session_count) sd_con_nbeac = sd_con_nbeac[~np.isnan(sd_con_nbeac)] sd_con_probe = np.nanstd(((firststopstoreprobe)), axis=1) / math.sqrt(session_count) sd_con_probe = sd_con_probe[~np.isnan(sd_con_probe)] # PLOT GRAPHS b_trial_max = np.arange(0,len(con_beac),1) nb_trial_max = np.arange(0,len(con_nbeac),1) p_trial_max = np.arange(0,len(sd_con_probe),1) # array of days #x = con_beac[0] # plot average first stop over days for all mice fig = plt.figure(figsize = (12,4)) # make figure, this shape (width, height) ax = fig.add_subplot(1,3,1) ax.set_title('Beaconed', fontsize=20, verticalalignment='bottom', style='italic') #title ax.axhspan(rz_start, rz_end, facecolor='g', alpha=0.15, hatch='/',linewidth=0) # green box of reward zone ax.axhspan(0, 4, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box (4 is used for appearance) ax.axhline(4, linewidth=1, ls='--', color='black') # mark black box border ax.axvline(0, linewidth=3, color='black') # bold line on the y axis ax.axhline(2, linewidth=3, color='black') # bold line on the x axis ax.plot(b_trial_max, con_beac, 'o',color = '0.3', label = 'Non reward zone score', linewidth = 2, markersize = 6, markeredgecolor = 'black') ax.errorbar(b_trial_max,con_beac,sd_con_beac, fmt = 'o', color = '0.3', capsize = 1.5, markersize = 2, elinewidth = 1.5) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =15) # tick parameters: pad is tick label relative to ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =15) ax.set_xlim(0,len(b_trial_max)) ax.set_ylim(2,rz_end+2) adjust_spines(ax, ['left','bottom']) # remove right and top axis plt.locator_params(nbins=7, axis ='y') # set tick number on y axis plt.locator_params(nbins=3, axis ='x') # set tick number on x axis ax = plt.ylabel('Location (VU)', fontsize=16, labelpad = 18) ax = fig.add_subplot(1,3,2) ax.set_title('Non-Beaconed', fontsize=20, verticalalignment='bottom', style='italic') ax.axhspan(rz_start, rz_end, facecolor='g', alpha=0.15, hatch='/', linewidth=0) # green box spanning the rewardzone - to mark reward zone ax.axhspan(0, 4, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box ax.axhline(4, linewidth=1, ls='--', color='black') # mark black box border ax.axvline(0, linewidth = 3, color = 'black')# bold line on the y axis ax.axhline(2, linewidth = 3, color = 'black')# bold line on the x axis ax.plot(nb_trial_max, con_nbeac, 'o', color = '0.3', label = 'Non reward zone score', linewidth = 2, markersize = 6, markeredgecolor = 'black') ax.errorbar(nb_trial_max,con_nbeac,sd_con_nbeac, fmt = 'o', color = '0.3', capsize = 1.5, markersize = 2, elinewidth = 1.5) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =15) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =15) ax.set_xlim(0,len(nb_trial_max)) ax.set_ylim(2,rz_end+2) adjust_spines(ax, ['left','bottom']) # remove right and top axis plt.locator_params(nbins=7, axis ='y') # set tick number on y axis plt.locator_params(nbins=3, axis ='x') # set tick number on x axis ax = plt.xlabel('Number of trials', fontsize=16,labelpad=18) ax = fig.add_subplot(1,3,3) ax.set_title('Probe', fontsize=20, verticalalignment='bottom', style='italic') # title ax.axhspan(rz_start, rz_end, facecolor='g', alpha=0.15, hatch='/', linewidth=0) # green box of reward zone ax.axhspan(0, 4, facecolor='k', alpha=0.15, hatch='/', linewidth=0) # black box (4 is used for appearance) ax.axhline(4, linewidth=1, ls='--', color='black') # mark black box border ax.axvline(0, linewidth=3, color='black') # bold line on the y axis ax.axhline(2, linewidth=3, color='black') # bold line on the x axis ax.plot(p_trial_max, con_probe, 'o', color = '0.3', label = 'Non reward zone score', linewidth = 2, markersize = 6, markeredgecolor = 'black') ax.errorbar(p_trial_max,con_probe,sd_con_probe, fmt = 'o', color = '0.3', capsize = 1.5, markersize = 2, elinewidth = 1.5) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =15) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =15) ax.set_xlim(0,len(p_trial_max)) ax.set_ylim(2,rz_end+2) adjust_spines(ax, ['left','bottom']) # remove right and top axis plt.locator_params(nbins=7, axis ='y') # set tick number on y axis plt.locator_params(nbins=3, axis ='x') # set tick number on x axis plt.subplots_adjust(hspace = .35, wspace = .35, bottom = 0.25, left = 0.15, right = 0.82, top = 0.85) fig.savefig(save_path, dpi=200) plt.close()
def plot_fig1G (session_paths, save_path): days = [1] # number_of_trials = 1000 # arbitrarily large amount of trials so we can catch all the trials # Arrays for storing data (output) firststopstorebeac = np.zeros(((number_of_trials), len(session_paths))) firststopstorenbeac = np.zeros(((number_of_trials), len(session_paths))) firststopstoreprobe = np.zeros(((number_of_trials), len(session_paths))) firststopstorebeac[:,:] = np.nan firststopstorenbeac[:,:] = np.nan firststopstoreprobe[:,:] = np.nan sd_con_firststopstorebeac = np.zeros(((number_of_trials), len(session_paths))) sd_con_firststopstorenbeac = np.zeros(((number_of_trials), len(session_paths))) sd_con_firststopstoreprobe = np.zeros(((number_of_trials), len(session_paths))) sd_con_firststopstorebeac[:,:] = np.nan sd_con_firststopstorenbeac[:,:] = np.nan sd_con_firststopstoreprobe[:,:] = np.nan # For each day and mouse, pull raw data, calculate first stops and store data for dcount, day in enumerate(days): session_count = 0 for session_path in session_paths: saraharray, track_start, track_end = translate_to_legacy_format(session_path) rz_start = saraharray[0, 11] rz_end = saraharray[0, 12] # make array of trial number for each row in dataset trialarray = maketrialarray(saraharray) # write array of trial per row in datafile saraharray[:,9] = trialarray[:,0] # replace trial column in dataset *see README for why this is done* # get stops and trial arrays dailymouse_b = np.delete(saraharray, np.where(saraharray[:, 8] > 0), 0) # delete all data not on beaconed tracks dailymouse_nb = np.delete(saraharray, np.where(saraharray[:, 8] != 10), 0)# delete all data not on non beaconed tracks dailymouse_p = np.delete(saraharray, np.where(saraharray[:, 8] != 20), 0)# delete all data not on # get stops stops_b = extractstops_HUMAN(dailymouse_b) stops_nb = extractstops_HUMAN(dailymouse_nb) stops_p= extractstops_HUMAN(dailymouse_p) # filter stops stops_b = filterstops(stops_b) stops_nb = filterstops(stops_nb) stops_p = filterstops(stops_p) if stops_b.size > 0: trialids_b = np.unique(stops_b[:, 2]) # make array of unique trial numbers for i in range(len(stops_b)): srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stops_b,trialids_b) # get average real stops & shuffled stops per lcoation bin shuff_beac = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) # calculate z-scores bb = shuff_beac[3]; rz = shuff_beac[9] # black box - reward zone zscore score = rz - bb if stops_nb.size > 0: trialids_nb = np.unique(stops_nb[:, 2]) # make array of unique trial numbers srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stops_nb,trialids_nb) # get average real stops & shuffled stops per lcoation bin shuff_nbeac = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) # calculate z-scores bb = shuff_nbeac[3]; rz = shuff_nbeac[9] # black box - reward zone zscore score = rz - bb for i in range(len(stops_nb)): firststopstorebeac[i, session_count] = score[i][0] if stops_p.size > 0: trialids_p = np.unique(stops_p[:, 2]) # make array of unique trial numbers srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stops_p,trialids_p) # get average real stops & shuffled stops per lcoation bin shuff_probe = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) # calculate z-scores bb = shuff_probe[3]; rz = shuff_probe[9] # black box - reward zone zscore score = rz - bb firststopstoreprobe[dcount, mcount] = score # store data mcount += 1 # get average real stops & shuffled stops per location bin zscore_b = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) for i in range(len(stops_b)): firststopstorebeac[i, session_count] = zscore_b[i][0] if stops_nb.size>0: trialids_nb = np.unique(stops_nb[:, 2]) srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stops_nb,trialids_nb) # get average real stops & shuffled stops per location bin zscore_nb = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) for i in range(len(stops_nb)): firststopstorebeac[i, session_count] = zscore_nb[i][0] if stops_p.nb.size>0: trialids_p = np.unique(stops_p[:, 2]) srbin_mean, srbin_std, shuffled_mean, shuffled_std = shuffle_analysis_pertrial3(stops_p,trialids_p) # get average real stops & shuffled stops per location bin zscore_p = z_score1(srbin_mean, srbin_std, shuffled_mean, shuffled_std) for i in range(len(stops_p)): firststopstorebeac[i, session_count] = zscore_p[i][0] session_count +=1 # stack experiments then average over days for each mouse con_b = np.nanmean(((firststopstorebeac)), axis = 1) con_b = con_b[~np.isnan(con_b)] con_nb = np.nanmean(((firststopstorenbeac)), axis =1) con_nb = con_nb[~np.isnan(con_nb)] con_p = np.nanmean(((firststopstoreprobe)), axis = 1) con_p = con_p[~np.isnan(con_nb)] sd_con_b = np.nanstd(((firststopstorebeac)), axis=1)/math.sqrt(session_count) sd_con_b = sd_con_b[~np.isnan(sd_con_b)] sd_con_nb = np.nanstd(((firststopstorenbeac)), axis=1)/math.sqrt(session_count) sd_con_nb = sd_con_nb[~np.isnan(sd_con_nb)] sd_con_p = np.nanstd(((firststopstoreprobe)), axis=1)/math.sqrt(session_count) sd_con_p = sd_con_p[~np.isnan(sd_con_p)] # PLOT GRAPHS bins = np.arange(0.5,21.5+1e-6,1) # track bins fig = plt.figure(figsize = (12,3)) ax = fig.add_subplot(1,3,1) ax.axvline(0, linewidth = 3, color = 'black') # bold line on the y axis ax.axhline(-10, linewidth = 3, color = 'black') # bold line on the x axis ax.axhline(0, linewidth = 1,ls='--', color = 'black') # bold line on the x axis ax.plot(bins,con_b,'o',color = 'Black',label = 'AAV-fl-GFP', linewidth = 2, markersize = 6, markeredgecolor = 'black') #plot becaoned trials ax.errorbar(bins,con_b,sd_con_b, fmt = 'o', color = 'black', capsize = 2, capthick = 1, markersize = 4, elinewidth = 1.5) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.set_xlim(0,22) ax.set_ylim(-10,20) adjust_spines(ax, ['left','bottom']) # removes top and right spines ax.locator_params(axis = 'x', nbins=3) # set number of ticks on x axis ax.locator_params(axis = 'y', nbins=4) # set number of ticks on y axis ax = plt.ylabel('Training day)', fontsize=16, labelpad = 18) ax = fig.add_subplot(1,3,2) #stops per trial ax.axvline(0, linewidth = 3, color = 'black') # bold line on the y axis ax.axhline(-10, linewidth = 3, color = 'black') # bold line on the x axis ax.axhline(0, linewidth = 1,ls='--', color = 'black') # bold line on the x axis ax.plot(bins,con_nb,'o', color = 'Black', linewidth = 2, markersize = 6, markeredgecolor = 'black') #plot becaoned trials ax.errorbar(bins,con_nb,sd_con_nb, fmt = 'o', color = 'black', capsize = 2, capthick = 1, markersize = 4, elinewidth = 1.5) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.set_xlim(0,22) ax.set_ylim(-10,20) adjust_spines(ax, ['left','bottom']) # re;moves top and right spines ax.locator_params(axis = 'x', nbins=3) # set number of ticks on x axis ax.locator_params(axis = 'y', nbins=4) # set number of ticks on y axis ax = plt.xlabel('Training day', fontsize=16, labelpad = 18) ax = fig.add_subplot(1,3,3) #stops per trial ax.axhline(0, linewidth = 1,ls='--', color = 'black') # bold line on the x axis ax.axvline(0, linewidth = 3, color = 'black') # bold line on the y axis ax.axhline(-10, linewidth = 3, color = 'black') # bold line on the x axis ax.plot(bins,con_p, 'o', color = 'Black',label = 'Beaconed', linewidth = 2, markersize = 6, markeredgecolor = 'black') #plot becaoned trials ax.errorbar(bins,con_p,sd_con_p, fmt = 'o', color = 'black', capsize = 2, capthick = 1, markersize = 4, elinewidth = 1.5) ax.tick_params(axis='x', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.tick_params(axis='y', pad = 10, top='off', right = 'off', direction = 'out',width = 2, length = 7,labelsize =16) ax.set_xlim(0,22) ax.set_ylim(-10,20) adjust_spines(ax, ['left','bottom']) # removes top and right spines ax.locator_params(axis = 'x', nbins=3) # set number of ticks on x axis ax.locator_params(axis = 'y', nbins=4) # set number of ticks on y axis ax = plt.xlabel('Training day', fontsize=16, labelpad = 18) plt.subplots_adjust(hspace = .35, wspace = .35, bottom = 0.25, left = 0.15, right = 0.82, top = 0.85) fig.savefig(save_path, dpi=200) plt.close()