Last plot in subplot becomes over-sized - matlab

Question

I am using subplot function of MATLAB. Surprisingly the last plot in each subplot set becomes over-sized. Can anybody help me to resolve this issue? I have experimented with the parameters a little, but no luck. I am not able to post the plot figure.
function plotFluxVariabilityByGene(cRxn,KeggID,geneName)
load iJO1366; % Load the model iJO1366
%Find 'Gene' associated reactions from 'model'
reactions = rxnNamesFromKeggID(model,KeggID);
nCheck = 0; % Initialize counter
% Determine initial subplot dimensions
[R C setSize] = subplotSize(numel(reactions));
for n = 1 : numel(reactions)
% Get the name of nth reaction
rxn = reactions{n};
% Define the array for control reaction fluxes
cRxnArray = getCrxnArray(model,cRxn);
% Initialize storage for lower and upper limit-values
L = []; U = []; Avg = [];
% Get the fluxVariability values
for i = 1 : numel(cRxnArray)
modelMod = changeRxnBounds(model,cRxn,cRxnArray(i),'b');
[L(i) U(i)] = fluxVariability(modelMod,100,'max',{rxn});
Avg(i) = (L(i) + U(i))/2;
%fprintf('mthfcFlux = %f; Li = %f; Ui = %f\n',array(i),L(i),U(i));
end
% adjust the subplot number
nCheck = nCheck + 1;
% Determine the range of n to be saved in one file
if nCheck == 1
start = n;
elseif nCheck == setSize;
stop = n;
end
subplot(R,C,nCheck)
plot(cRxnArray,L,'-r','LineWidth',1); hold on;
plot(cRxnArray,L,'^r','MarkerSize',3,'LineWidth',2);
plot(cRxnArray,U,'-.b','LineWidth',1);
plot(cRxnArray,U,'^b','MarkerSize',2,'LineWidth',2);
plot(cRxnArray,Avg,'-','Color',[0.45,0.45,0.45],'LineWidth',2.5);
% Label X and Y axes
%xlabel([cRxn ' Flux']);
%ylabel(['fluxVariability ' char(rxn)]);
xlabel('Flux');
ylabel('fluxVariability');
hold off;
% Adjust X and Y axes limits
%xmn = min(cRxnArray) - ((max(cRxnArray) - min(cRxnArray))*0.05);
%xmx = max(cRxnArray) + ((max(cRxnArray) - min(cRxnArray))*0.05);
%ymn = min([U L]) - ((max([U L]) - min([U L]))*0.05);
%ymx = max([U L]) + ((max([U L]) - min([U L]))*0.05);
%if xmn ~= xmx
% xlim([xmn xmx]);
%end
%if ymn ~= ymx
% ylim([ymn ymx]);
%end
% Print which reactions are done
fprintf('\n......done for %s',char(rxn));
% If 'setSize' subplots are done then save the set in a file
if nCheck == setSize
saveas(gcf,['TEST/' cRxn 'flux-Vs-' geneName '_fluxVariability' num2str(start) '-' num2str(stop) '.fig']);
saveas(gcf,['TEST/' cRxn 'flux-Vs-' geneName '_fluxVariability' num2str(start) '-' num2str(stop) '.eps']); close(gcf);
% Determine initial subplot dimensions
[R C setSize] = subplotSize(numel(reactions)-n);
% Return nCheck to zero;
nCheck = 0;
end
end
% If nCheck is not equal to 16 then there are subplot that is not saved
% inside the for loop. Let's save it here.
if nCheck ~= setSize
stop = n;
saveas(gcf,['TEST/' cRxn 'flux-Vs-' geneName '_fluxVariability' num2str(start) '-' num2str(stop) '.fig']);
saveas(gcf,['TEST/' cRxn 'flux-Vs-' geneName '_fluxVariability' num2str(start) '-' num2str(stop) '.eps']); close(gcf);
end
fprintf('\nAll done\n');
end
%####################################################
%# Other functions ##
%####################################################
function rxnNames = rxnNamesFromKeggID(model,KeggID)
% Find 'Gene' associated reactions from 'model'
associatedRxns = findRxnsFromGenes(model,KeggID);
% Extract the reaction details from the structure to a cell
rxnDetails = eval(sprintf('associatedRxns.%s',KeggID));
% Extract only the reaction names from the cell
rxnNames = rxnDetails(:,1);
end
%####################################################
function cRxnArray = getCrxnArray(model,cRxn)
% Define the solver
changeCobraSolver('glpk');
% Find solution for the model
sol = optimizeCbModel(model);
% Change the objective of the default model to 'cRxn'
tmpModel = changeObjective(model,cRxn);
% Find slution for the changed model. This gives the maximum and
% minimum possible flux through the reaction 'cRxn' when the model is
% still viable
%solMax = optimizeCbModel(tmpModel,'max');
solMin = optimizeCbModel(tmpModel,'min');
% Create an array of 20 euqally spaced flux values between 'solMin' and
% 'sol.x'
%array = linspace(solMin.f,solMax.f,10);
cRxnArray = linspace(solMin.f,sol.x(findRxnIDs(model,cRxn)),20);
end
%####################################################
function [R C setSize] = subplotSize(remainingPlots)
% Sets number of columns and rows to 3 if total subplot >= 9
if remainingPlots > 7
R = 3; C = 3; setSize = 9;
elseif remainingPlots < 7
R = 2; C = 3; setSize = 6;
elseif remainingPlots < 5
R = 2; C = 2; setSize = 4;
elseif remainingPlots < 4
R = 1; C = 3; setSize = 3;
elseif remainingPlots < 3
R = 1; C = 2; setSize = 2;
end
end
%####################################################
My subplot looks like this:

Answer 1

I suspect its because you are calling subplotSize a second time inside your loop. This could be changing your R and C variables.
I would advise to check the R and C variables at the subplot command on each loop.