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figure4_supp_curated_vs_raw.m
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figure4_supp_curated_vs_raw.m
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%figure 4 - figure supplement comparing yield in curated versus uncurated data
% (in response to major comment 5)
P=get_parameters;
exclude_3A=true;
normalize_by_electrode=true;
from_scratch = false; % regenerate the data files?
if from_scratch
%------------below code requires raw data not included in repo
%% get the curated data
Cells_curated = collect_cells_files('curated');
Cells_curated=postprocess_Cells(Cells_curated);
T_curated = get_metrics_from_Cells(Cells_curated,'exclude_3A',exclude_3A);
%% get the matching uncurated data
Cells_uncurated = collect_cells_files('uncurated_matching_curated');
Cells_uncurated = postprocess_Cells(Cells_uncurated);
T_uncurated = get_metrics_from_Cells(Cells_uncurated,'exclude_3A',exclude_3A);
%--------------
save(P.curation_comparison_data_path,'T_curated','T_uncurated');
else
load(P.curation_comparison_data_path);
end
%% unit info
uncurated_units = [T_uncurated.unit];
curated_units = [T_curated.unit];
uncurated_single_units = [T_uncurated.single_unit];
curated_single_units = [T_curated.single_unit];
days_elapsed = [T_curated.days_elapsed];
n_elec = [T_uncurated.n_elec];
unit_ratio = curated_units./uncurated_units;
single_unit_ratio = curated_single_units./uncurated_single_units;
%% Set up the figue
figure('Pos', [100, 50, 700, 1500]);
k = 0;
positions = {[0.14 0.85 0.33 0.14],... %A
[0.64 0.85 0.33 0.14],... %B
[0.14 0.65 0.33 0.14],... %C
[0.64 0.65 0.33 0.14],... %D
[0.14 0.45 0.33 0.14],... %E
[0.64 0.45 0.33 0.14],... %F
[0.14 0.25 0.33 0.14],... %G
[0.64 0.25 0.33 0.14],... %H
[0.14 0.05 0.33 0.14],... %I
[0.64 0.05 0.33 0.14]}; %J
%% A: plot units for uncurated
k=k+1;
subplot('position',positions{k});
plot_indiv_identifier(T_uncurated,'legend_on',false,'metric','unit','normalize_by_electrode',normalize_by_electrode);
text(1,max(ylim)*0.9,'uncurated','FontSize',P.font_size);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% B: plot SU, uncurated
k=k+1;
subplot('position',positions{k});
plot_indiv_identifier(T_uncurated,'legend_on',false,'metric','single_unit','normalize_by_electrode',normalize_by_electrode);
text(1,max(ylim)*0.9,'uncurated','FontSize',P.font_size);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% C: plot units for curated
k=k+1;
subplot('position',positions{k});
plot_indiv_identifier(T_curated,'legend_on',false,'metric','unit','normalize_by_electrode',normalize_by_electrode);
text(1,max(ylim)*0.9,'curated','FontSize',P.font_size);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% D: plot SU, uncurated
k=k+1;
subplot('position',positions{k});
plot_indiv_identifier(T_curated,'legend_on',false,'metric','single_unit','normalize_by_electrode',normalize_by_electrode);
text(1,max(ylim)*0.9,'curated','FontSize',P.font_size);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% E: plot units scatter
k=k+1;
subplot('position',positions{k});
if normalize_by_electrode
scatter(uncurated_units./n_elec,curated_units./n_elec,40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
xlabel({'Units/electrode','before curation'});
ylabel({'Units/electrode','after curation'});
else
scatter(uncurated_units,curated_units,40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
xlabel('Units before curation');
ylabel('Units after curation');
end
[r,p] = corrcoef(uncurated_units,curated_units);
stats_label=sprintf('r = %0.2g\np = %0.2g',r(2),p(2));
text(0.25,1.6,stats_label,'FontSize',P.font_size);
set(gca,P.axes_properties{:});h=refline(1,0);h.LineWidth=1;h.Color=[0 0 0];
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% F: plot SU scatter
k=k+1;
subplot('position',positions{k});
if normalize_by_electrode
scatter(uncurated_single_units./n_elec,curated_single_units./n_elec,40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
xlabel({'Single units/electrode','before curation'});
ylabel({'Single units/electrode','after curation'});
else
scatter(uncurated_single_units,curated_single_units,40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
xlabel('Single units before curation');
ylabel('Single units after curation');
end
[r,p] = corrcoef(uncurated_single_units,curated_single_units);
stats_label=sprintf('r = %0.2g\np = %0.2g',r(2),p(2));
text(0.09,0.8,stats_label,'FontSize',P.font_size);
set(gca,P.axes_properties{:});h=refline(1,0);h.LineWidth=1;h.Color=[0 0 0];
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% G: plot ratio against uncurated unit conut
k=k+1;
subplot('position',positions{k});
scatter(uncurated_units./n_elec,[T_curated.unit]./[T_uncurated.unit],40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
[r,p] = corrcoef(log10([T_uncurated.unit]),[T_curated.unit]./[T_uncurated.unit]);
stats_label=sprintf('r = %0.2g\np = %0.2g',r(2),p(2));
text(1.2,1.3,stats_label,'FontSize',P.font_size);
ylabel({'curated/uncurated','unit ratio'});
xlabel({'Units/electrode','before curation'});
set(gca,P.axes_properties{:},'ylim',[0 2]);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% H: plot ratio against uncurated single unit conut
k=k+1;
subplot('position',positions{k});
scatter(uncurated_single_units./n_elec,[T_curated.single_unit]./[T_uncurated.single_unit],40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
[r,p] = corrcoef(log10([T_uncurated.single_unit]),[T_curated.single_unit]./[T_uncurated.single_unit]);
stats_label=sprintf('r = %0.2g\np = %0.2g',r(2),p(2));
text(0.6,1.3,stats_label,'FontSize',P.font_size);
ylabel({'curated/uncurated','single unit ratio'});
xlabel({'Single units/electrode','before curation'});
set(gca,P.axes_properties{:},'ylim',[0 2]);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% I: plot ratio against days implanted, units
k=k+1;
subplot('position',positions{k});
scatter(days_elapsed,unit_ratio,40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
[r,p] = corrcoef(log(days_elapsed),unit_ratio);
stats_label=sprintf('r = %0.2g\np = %0.2g',r(2),p(2));
text(26,0.3,stats_label,'FontSize',P.font_size);
ylabel({'curated/uncurated','unit ratio'});
xlabel('Days since implant');
set(gca,P.axes_properties{:},P.custom_axes_properties.longevity{:},'xscale','log','ylim',[0 2]);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
%% J: plot ratio against days implanted, single units
k=k+1;
subplot('position',positions{k});
scatter(days_elapsed,single_unit_ratio,40,'markeredgecolor','k','markerfacecolor','none','linewidth',1);
[r,p] = corrcoef(log(days_elapsed),single_unit_ratio);
stats_label=sprintf('r = %0.2g\np = %0.2g',r(2),p(2));
text(26,0.3,stats_label,'FontSize',P.font_size);
ylabel({'curated/uncurated','single unit ratio'});
xlabel('Days since implant');
set(gca,P.axes_properties{:},P.custom_axes_properties.longevity{:},'xscale','log','ylim',[0 2]);
label_hdl(k)=label_panel(gca, P.panel_labels(k), 'FontSize', P.panel_label_font_size);
% standardize label position
for i = 1:numel(label_hdl)
label_hdl(i).Position(1) = label_hdl(i).Position(1)+0.02;
label_hdl(i).Position(2) = label_hdl(i).Position(2)-0.02;
if i==6 || i==8 || i==10
label_hdl(i).Position(1)=label_hdl(4).Position(1);
end
if i<3
label_hdl(i).Position(2)=label_hdl(4).Position(2)+0.175;
end
end
for i = 1:numel(P.figure_image_format)
saveas(gcf, [P.plots_folder_path filesep mfilename], P.figure_image_format{i})
end