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mydata_shstat.m
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mydata_shstat.m
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%% mydata_shstat: demo script for using plotting tool shstat
% see prt_pars for more examples of 1D plotting
%
% Make sure that the lists-of-lists correspond with allStat.mat.
% Generate updated allStat.mat if necessary (for curators only)
% write_allStat(C2K(20),1); % notice that default allStat is at T=T_typical and f=1
% allStat has fields for the temp-correction c_T, so divide rates by c_T to go from T_typical to T_ref
%
% Compose/modify your legend if you wish. You can also do this on-the-fly by selecting an empty legend.
% mylegend = select_legend; replace legend_* by mylegend in the examples below, to activate this.
% If your desired legend is close to an existing one, e.g. legend_fish, you can modify it by: mylegend = select_legend(legend_fish)
close all % remove any existing figure
example = 4; % edit this number to see the various examples
switch example
case 1 % 2D: use default settings
shstat_options('default');
shstat({'E_Hp', 'E_Hb'}, legend_RSED);
case 2 % 2D: more tricks: no transformation (default is log10), description enabled, adding items to the figure
shstat_options('default');
shstat_options('x_transform', 'none');
shstat_options('y_transform', 'none');
shstat_options('x_label', 'on');
shstat_options('y_label', 'on');
[Hfig Hleg] = shstat({'s_s', 'kap'}, legend_vert, date); % set title, output handle for adding items
figure(Hfig) % add items to figure
kap = linspace(0, 1, 100); ss = kap.^2 .* (1 - kap);
plot(ss, kap, 'k', 'Linewidth', 2)
xlim([0 4/27]); ylim([0 1]);
case 3 % 2D: like 2, but with logarithmic transformation on independent variable only
shstat_options('default');
shstat_options('y_transform', 'none');
shstat_options('x_label', 'on');
shstat_options('y_label', 'on');
[Hfig Hleg] = shstat({'s_s', 'kap'}, legend_RSED); % output handle for adding items
figure(Hfig) % add items to figure
kap = linspace(1e-6,1,100); ss = kap.^2 .* (1 - kap);
plot(log10(ss), kap, 'k', 'Linewidth', 2)
ylim([0 1]);
case 4 % 3D: hit rotation-tool in the toolbar of the figure
shstat_options('default');
shstat_options('x_transform', 'none');
shstat_options('y_transform', 'none');
shstat_options('z_transform', 'none');
[Hfig Hleg] = shstat({'kap', 'ep_min', 's_s'}, legend_vert); % output handle for adding items
figure(Hfig) % add items to figure
kap = linspace(0, 1, 15)'; f = kap'; ss = kap.^2 .* (1 - kap) * f.^3; % set x,y,z values
mesh(kap, f, ss'); % add surface to figure
% define colormap for mesh: k->b->m->r->white
Colmap = [0 0 0; 0 0 .5; 0 0 1; .5 0 1; 1 0 1; 1 0 .5; 1 0 0; 1 .25 .25; 1 .5 .5; 1 .75 .75];
colormap(Hfig, Colmap) % set color map to add_my_pet colors
zlim([0 4/27])
case 5 % 2D: numerical mode because of computations: setting of xlabel and ylabel required
shstat_options('default');
shstat_options('x_transform', 'none');
shstat_options('y_transform', 'none');
essk = read_allStat('ep_min', 's_s', 's_M', 'kap'); ep_min = essk(:,1); s_s = essk(:,2); s_M = essk(:,3); kap = essk(:,4);
[Hfig Hleg] = shstat([ep_min, (s_s ./ (kap.^2 .* (1 - kap))) .^(1/3)], legend_vert); % output handle for setting labels
figure(Hfig) % add labels to figure, because this is not done by shstat in numerical mode
xlabel('e_p^{min}, -')
ylabel('max e_p^{min}, -')
case 6 % 1D: single variable with default colors
shstat_options('default');
shstat_options('x_transform', 'none');
shstat_options('y_label', 'on'); % if 'off' (default), no `survivor function' shown on yaxis
shstat({'kap'});
case 7 % 1D: numerical mode because of computations: setting of xlabel required
vsM = read_allStat('v', 's_M'); sM = vsM(:,2); vj = prod(vsM,2); v = vj(sM == 1); vj = vj(sM > 1);
shstat_options('default');
shstat_options('y_label', 'on'); % if 'off' (default), no `survivor function' shown on yaxis
Hfig = shstat(vj, {'r', 'r'}); % output handle for adding items to same figure and set colors
shstat(v, {'b', 'b'}, 'post-metam v at T_{ref} and f=1, without and with acceleration', Hfig);
% setting of figure handle not required, because legend is not shown in new figure, and first figure is still active
xlabel('_{10}log v, cm/d')
case 8 % 1D: single variable for several taxa with line specs specified by llegend_ACP
shstat_options('default');
shstat_options('x_transform', 'none');
shstat_options('y_label', 'on'); % if 'off' (default), no `survivor function' shown on yaxis
shstat({'kap'}, llegend_ACP);
case 9 % 2D: selection of different model types, rather than taxa; bypass shstat
% type, size, linewidth, edge color and face color of a marker, model
legend = {...
{'o', 8, 3, [0 0 0], [0 0 0]}, 'hep'; ...
{'o', 8, 3, [0 0 1], [0 0 1]}, 'hex'; ...
{'o', 8, 3, [0 0 1], [0 0 0]}, 'abj'; ...
{'o', 8, 3, [0 0 1], [1 0 1]}, 'asj'; ....
{'o', 8, 3, [0 0 1], [1 0 0]}, 'sbp'; ....
{'o', 8, 3, [1 0 1], [1 0 1]}, 'abp'; ....
{'o', 8, 3, [1 0 1], [1 0 0]}, 'ssj'; ....
{'o', 8, 3, [1 0 0], [0 0 0]}, 'stx'; ....
{'o', 8, 3, [1 0 0], [0 0 1]}, 'stf'; ....
{'.', 8, 3, [0 0 0], [0 0 0]}, 'std'; ....
};
n_model = size(legend,1);
vars = read_allStat('kap','v','s_M'); val_plot = [vars(:,1), log10(vars(:,2) .* vars(:,3))];
model = read_allStat('model'); % don't combine num and str in 1 call to read_allStat
entries = select; % assign entry names for clicking in plot
Hfig = 1; % set figure handle
figure(Hfig)
hold on
for j=1:n_model
i = n_model - j + 1; % reverse sequence of plotting in case markers overlap
marker = legend{i,1}; T = marker{1}; MS = marker{2}; LW = marker{3}; MEC = marker{4}; MFC = marker{5};
sel = strcmp(model, legend{i,2}); % select model type
plot(val_plot(sel,1), val_plot(sel,2), T, 'MarkerSize', MS, 'LineWidth', LW, 'MarkerFaceColor', MFC, 'MarkerEdgeColor', MEC)
end
set(gca, 'FontSize', 15, 'Box', 'on')
xlabel('\kappa, -')
ylabel('_{10}log v at T_{ref} post metam, cm/d')
h = datacursormode(Hfig); % write entry names under plot coordinates
h.UpdateFcn = @(obj, event_obj)xylabels(obj, event_obj, entries, val_plot);
datacursormode on % mouse click on plot
Hleg = shlegend(legend);
case 10 % 2D, numerical mode
shstat_options('default');
LmEm = read_allStat('L_m', 'E_m'); L_m = LmEm(:,1); E_m = LmEm(:,2);
[Hfig, Hleg] = shstat([L_m.^3, E_m], legend_fish, 'Data at T_{typical}');
figure(Hfig) % add labels to figure, because this is not done by shstat in numerical mode
xlabel('_{10} log max structural volume, L^3, cm^3')
ylabel('_{10} log max reserve capacity, [E_m], J/cm^3')
case 11 % 2D
shstat_options('default');
LmpM = read_allStat('L_m', 'p_M'); L_m = LmpM(:,1); p_M = LmpM(:,2);
[Hfig, Hleg] = shstat([L_m.^3, p_M], legend_RSED, 'Data at T_{typical}');
figure(Hfig) % add labels to figure, because this is not done by shstat in numerical mode
xlabel('_{10} log max structural volume, cm^3')
ylabel('_{10} log spec som maintenance, J/d.cm^3')
case 12 % 2D
shstat_options('default');
shstat_options('x_transform', 'none');
kEmdV = read_allStat('kap', 'E_m', 'd_V'); kap = kEmdV(:,1); E_m = kEmdV(:,2); d_V = kEmdV(:,3);
[Hfig, Hleg] = shstat([kap, E_m./d_V], legend_fish);
figure(Hfig) % add labels to figure, because this is not done by shstat in numerical mode
xlabel('kappa, -')
ylabel('_{10}log [E_m]/d_V , J/g')
case 13 % 3D/2D
shstat_options('default'); % log10 transform for all 3 variables
pM_pAm_Li = read_allStat('p_M', 'p_Am', 'L_i', 's_M'); p_M = pM_pAm_Li(:,1); p_Am = pM_pAm_Li(:,2) .* pM_pAm_Li(:,4); L_i = pM_pAm_Li(:,3);
[Hfig, Hleg] = shstat([p_M, p_Am, L_i], {{'^', 7, 2}, 'Sauropsida'; {'v', 7, 2}, 'Mammalia'; {'o', 7, 2}, 'Chordata'}); % define colorless legend on the fly
figure(Hfig) % add labels to figure, because this is not done by shstat in numerical mode
xlabel('_{10}log [p_M], J/d.cm^3')
ylabel('_{10}log \{p_{Am}\}, J/d.cm^2')
zlabel('_{10}log L_\infty , cm')
case 14 % 2D for eco-codes (because col 2 in legend is cell string, not character string)
shstat_options('default');
% B. stands for "Embryo environment" (see shstat); for codes, see AmPtool eco page (CONTEXT dropdown)
legend_eco = {...
{'o', 8, 3, [0 1 0], [0 1 0]}, {'B.Tnp','B.Tnw'}; .... % nest in shrubs, trees
{'o', 8, 3, [1 0 0], [1 0 0]}, {'B.Tnc'}; ... % nest on rock, cliffs
{'o', 8, 3, [0 0 1], [0 0 1]}, {'B.Tnf'}; ... % nest on fresh water
{'o', 8, 3, [0 0 0], [0 0 0]}, {'B.Tnt','B.Tns','B.Tl'}; ... % nest in/on soil, under leaves
};
% Plot maturity ratio at birth/puberty (S_Hbp) as function of age at puberty (ap), for birds (Aves)
[Hfig, Hleg, val, entries, missing] = shstat({'a_p','s_Hbp'}, legend_eco, 'Aves');
end