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Tutorial: Database analysis

Load example data

First download the example Matlab data file from here and load it like this:

load('supp_mat_2_dat.mat')

This will load a small experimental measurements dataset in several tests_db objects.

Example for averaging rows

Display example database contents before averaging (see Table 3A in manuscript):

displayRows(sortrows(raw_example1_db, 'pAcip'))

% average the rows
avg_example1_db = meanDuplicateParams(raw_example1_db);

% display contents after averaging
displayRows(sortrows(avg_example1_db, 'pAcip'))

% optionally, generate a formatted LaTeX table (see Table 3B in manuscript)
string2File(displayRowsTeX(sortrows(avg_example1_db, 'pAcip'), ...
                           'Parameter in the raw cell database.', ...
                           struct('rotate', 0, 'width', '\textwidth', ...
                                  'label', 'tbl:ttx-cells')), 'example-table.tex')

Example for combining (merging) rows

Display example database contents before merging (see Table S1A in manuscript)

displayRowsTeX(sortrows(merge_example_db, 'NeuronId'))

Merge columns into rows

merged_db = ...
   mergeMultipleCIPsInOne(delColumns(merge_example_db(:, :, 1), ...
				     {'NumDuplicates', 'RowIndex'}), ...
			  {'_0pA', 9, ...
			      '_D100pA', 9, '_D200pA', 9})

Display after merging

displayRowsTeX(sortrows(merged_db, 'NeuronId'))

Optionally, generate a formatted LaTeX table (see Table S1B in manuscript)

string2File(displayRowsTeX(sortrows(merged_db, 'NeuronId'), ...
                           'Parameter in the raw cell database.', ...
                           struct('rotate', 0, 'width', '\textwidth', ...
                                  'label', 'tbl:ttx-cells')), ['example-' ...
                    'table.tex'])

Example for invariant parameter effects

Display database contents of TTX cells (see Table 4 in manuscript)

displayRows(sortrows(ttx_example1_db, 'NeuronId'))

% select two TTX concentrations and three neurons

ttx_reduced_db = ttx_example1_db(anyRows(ttx_example1_db(:, 'TTX'), [0; ...
                    7e-9]) & anyRows(ttx_example1_db(:, 'NeuronId'), [107; ...
                   108; 110]), :)

% find invariant parameter effects on extracted characteristics

ttx_invar_reduced_db = invarParam(delColumns(ttx_reduced_db, 'TracesetIndex'), 'TTX')

% Find differential effects of TTX on rate

ttx_diffed_db = diff2D(ttx_invar_reduced_db, 'D100pA_steady_rate');

% Plot as a bar plot (Figure 8C in manuscript)

plotFigure(plotBox(ttx_diffed_db(:, 'd1_2'), '', ...
                   struct('quiet', 1, 'putLabels', 1, 'fixedSize', ...
                          [2.5 2], 'colormap', [0 0 0])))

% Find statistics of parameter effects

ttx_stats_db = statsMeanSE(swapRowsPages(ttx_invar_reduced_db));

% plot bar plot showing parameter effects (see Figure 8B in manuscript)

plotFigure(plot_bars(ttx_stats_db(:, {'TTX', 'D100pA_steady_rate'}, :), ...
                     '', ...
                     struct('pageVariable', 'TTX', 'axisLimits', [NaN NaN ...
                    20 30], 'quiet', 1, 'fixedSize', [2.5 2], 'colormap', ...
                            [0 0 0])))