I am trying to update a series of plots within a subplot in a GUI

I am programming a GUI to take in data from .dat files and graph them. The options should create a subplot with up to 3 selections being made meaning I can have 1 plot or up to 3 plots being displayed on an axes. Right now I can plot and see the correct plot for only the first iteration with successive plots being displayed in the figure window, or only have the plots being displayed in the figure window. My main point of contention is also the fact that I need to save a copy of the subplots later on.

I've attached my code but am unsure what to do to have consistent plotting within the window that does not plot in the matlab figure window at all.

handles.hfig = figure;
        guidata(hObject, handles);  
        
        %wind speed
        if windSpeedCheckValue == 1
            n = n+1;
            set(0,'CurrentFigure',handles.hfig);
            subplot(3,1,n);
%             hold on
            [tout, dataout] = average_data(t, H2O, 20*AveragingTime);
            plot(tout, dataout, 'LineWidth', LineWidth);
%             hold off
            datetick('x', 'HH:MM:SS');
            xlabel('t');
            ylabel('H_2O (mmol/m^3)');
            box on
            if n == 1
                title(date);
            end
        else
%             try
%                 %This gets rid of plot elements such as lines when specific
%                 %subpot not used
%                 children = get(handles.plot1, 'children');
%                 delete(children(1));
%                 %Hides the plot when checkbox not selected
%                 set(handles.plot1,'visible', 'off');
% %                 if windDirectionCheckValue == 1
% %                     set(handles.plot3,'visible', 'off');
% %                 end
%         
% %                 handles.plot1 = rmfield(handles, 'plot1');
%             end
        end
        
        %vertical wind speed
        if vertWindSpeedCheckValue == 1
            n = n+1;
            set(0,'CurrentFigure',handles.hfig);
            subplot(3,1,n);
%             hold on
            [tout, dataout] = average_data(t, H2Oabs, 20*AveragingTime);
            plot(tout, dataout, 'LineWidth', LineWidth);
%             hold off
            datetick('x', 'HH:MM:SS');
            xlabel('t');
            ylabel('H_2O Absorbance');
            box on
            if n == 1
                title(date);
            end
        else
%             try
%                 children = get(handles.plot2, 'children');
%                 delete(children(1));
%                 set(handles.plot2,'visible', 'off');
% %                 handles.plot2 = rmfield(handles, 'plot2');
%             end
        end

        %wind direction
        if windDirectionCheckValue == 1
%             try 
%                 if windSpeedCheckValue == 0
%                     set(handles.plot3,'visible', 'on');
%                 end
%             end
            n = n+1;
            set(0,'CurrentFigure',handles.hfig);
            subplot(axes,3,1,n);
%             hold on
            [tout, dataout] = average_data(t, P7500, 20*60);
            plot(tout, dataout, 'LineWidth', LineWidth);
%             hold off
            datetick('x', 'HH:MM:SS');
            xlabel('t');
            ylabel('P7500 (kPa)');
            box on
            if n == 1
                title(date);
            end
        else
%             try
%                 children = get(handles.plot3, 'children');
%                 delete(children(1));
%                 set(handles.plot3,'visible', 'off');
% %                 handles.plot3 = rmfield(handles, 'plot3');
%             end
        end
        
        %set the axis as the parent of the image within the imshow command
        imshow(handles.hfig,'Parent',handles.axes1);
        handles.saveFigure = findobj(gcf,'Type', 'figure');
        guidata(hObject, handles);