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NPCMaturation
Commit bddc56d1 authored by Antonio Politi's avatar Antonio Politi
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matlabcode/delayedEquationModel/absDelayedMaturation.m
View file @ bddc56d1
classdef absDelayedMaturation < handle
properties (Access = protected)
timeI = [0:150]; %intergration time points
dataA; %data structure containing array of all data
tpm; %time of postmitotic start for non-core NC and Core region [time_start_pm_NC time_start_pm_C]
ti; %time interphase assembly start [time_start_ip_NC time_start_ip_C]
end
properties
indir;
outdir;
dataF; %data structure containing data to be fitted
end
methods
function MO = absDelayedMaturation(force, showplot)
if nargin < 1
force = 0;
end
if nargin < 2
showplot = 0;
end
MO.dataA = MO.dataIn(force, showplot);
end
function dataA = dataIn(MO, force, showplot)
%read in mature and pre
if nargin < 1
force = 0;
end
if nargin < 2
showplot = 0;
end
if ispc
indir = fullfile([getenv('HOMEDRIVE') getenv('HOMEPATH') ], 'Dropbox', 'NPCMaturation',...
'expdata', 'emdata');
outdir = fullfile([getenv('HOMEDRIVE') getenv('HOMEPATH') ], 'Dropbox', 'NPCMaturation',...
'results', 'emdata');
end
if ismac
indir = fullfile(getenv('HOME'), 'Dropbox', 'NPCMaturation',...
'expdata', 'emdata');
outdir = fullfile(getenv('HOME'), 'Dropbox', 'NPCMaturation',...
'results', 'emdata');
end
MO.indir = indir;
MO.outdir = outdir;
matfile = fullfile(indir,'emdata.mat');
if exist(matfile) && ~force
load(matfile)
return
end
% first entry is minipore second entry is mature pore
data = struct('time', [], 'd_noncore', [], 'd_core_i', [], 'd_core_o', [], 't_core_i', [], 't_core_o', []);
dataA = [data; data];
xlsfile = fullfile(indir, 'Minipore-number-to-Antonio-141022.xlsx');
dataA(2).time = xlsread(xlsfile, 'Onlyvalues', 'C4:C15');
dataA(2).t_noncore = xlsread(xlsfile, 'Onlyvalues', 'D4:E15');
dataA(2).t_core_i = xlsread(xlsfile, 'Onlyvalues', 'F4:G15');
dataA(2).t_core_o = xlsread(xlsfile, 'Onlyvalues', 'H4:I15');
dataA(2).d_noncore = xlsread(xlsfile, 'Onlyvalues', 'D20:E31');
dataA(2).d_core_i = xlsread(xlsfile, 'Onlyvalues', 'F20:F31');
dataA(2).d_core_o = xlsread(xlsfile, 'Onlyvalues', 'H20:I31');
dataA(1).time = xlsread(xlsfile, 'Onlyvalues', 'K4:K15');
dataA(1).t_noncore = xlsread(xlsfile, 'Onlyvalues', 'L4:M15');
dataA(1).t_core_i = xlsread(xlsfile, 'Onlyvalues', 'N4:O15');
dataA(1).t_core_o = xlsread(xlsfile, 'Onlyvalues', 'P4:Q15');
dataA(1).d_noncore = xlsread(xlsfile, 'Onlyvalues', 'L20:M31');
dataA(1).d_core_i = xlsread(xlsfile, 'Onlyvalues', 'N20:O31');
dataA(1).d_core_o = xlsread(xlsfile, 'Onlyvalues', 'P20:Q31');
%% read and create surface area
surfdatafile = fullfile(indir, 'surfaceNucleus_24h_new.txt');
surfdata = load(surfdatafile);
dataA(1).surf = [surfdata(:,1)*60 surfdata(:,2:3)];
dataA(1).surf = [0 surfdata(1,2:3); dataA(1).surf];
% perform a spline fit to smooth the data
dataA(1).surfspl = surfSpline( dataA(1).surf(:,1), dataA(1).surf(:,2),7, 3, 8);
dataA(1).dsurfspl = fnder(dataA(1).surfspl, 1);
save(matfile, 'dataA');
end
end
end
classdef absDelayedMaturation < handle
properties (Access = protected)
timeI = [0:150]; %intergration time points
dataA; %data structure containing array of all data
tpm; %time of postmitotic start for non-core NC and Core region [time_start_pm_NC time_start_pm_C]
ti; %time interphase assembly start [time_start_ip_NC time_start_ip_C]
end
properties
indir;
outdir;
dataF; %data structure containing data to be fitted
end
methods
function MO = absDelayedMaturation(force, showplot)
if nargin < 1
force = 0;
end
if nargin < 2
showplot = 0;
end
MO.dataA = MO.dataIn(force, showplot);
end
function dataA = dataIn(MO, force, showplot)
%read in mature and pre
if nargin < 1
force = 0;
end
if nargin < 2
showplot = 0;
end
if ispc
indir = fullfile([getenv('HOMEDRIVE') getenv('HOMEPATH') ], 'Dropbox', 'NPCMaturation',...
'expdata', 'emdata');
outdir = fullfile([getenv('HOMEDRIVE') getenv('HOMEPATH') ], 'Dropbox', 'NPCMaturation',...
'results', 'emdata');
end
if ismac
indir = fullfile(getenv('HOME'), 'Dropbox', 'NPCMaturation',...
'expdata', 'emdata');
outdir = fullfile(getenv('HOME'), 'Dropbox', 'NPCMaturation',...
'results', 'emdata');
end
MO.indir = indir;
MO.outdir = outdir;
matfile = fullfile(indir,'emdata.mat');
if exist(matfile) && ~force
load(matfile)
return
end
% first entry is minipore second entry is mature pore
data = struct('time', [], 'd_noncore', [], 'd_core_i', [], 'd_core_o', [], 't_core_i', [], 't_core_o', []);
dataA = [data; data];
xlsfile = fullfile(indir, 'Minipore-number-to-Antonio-141022.xlsx');
dataA(2).time = xlsread(xlsfile, 'Onlyvalues', 'C4:C15');
dataA(2).t_noncore = xlsread(xlsfile, 'Onlyvalues', 'D4:E15');
dataA(2).t_core_i = xlsread(xlsfile, 'Onlyvalues', 'F4:G15');
dataA(2).t_core_o = xlsread(xlsfile, 'Onlyvalues', 'H4:I15');
dataA(2).d_noncore = xlsread(xlsfile, 'Onlyvalues', 'D20:E31');
dataA(2).d_core_i = xlsread(xlsfile, 'Onlyvalues', 'F20:F31');
dataA(2).d_core_o = xlsread(xlsfile, 'Onlyvalues', 'H20:I31');
dataA(1).time = xlsread(xlsfile, 'Onlyvalues', 'K4:K15');
dataA(1).t_noncore = xlsread(xlsfile, 'Onlyvalues', 'L4:M15');
dataA(1).t_core_i = xlsread(xlsfile, 'Onlyvalues', 'N4:O15');
dataA(1).t_core_o = xlsread(xlsfile, 'Onlyvalues', 'P4:Q15');
dataA(1).d_noncore = xlsread(xlsfile, 'Onlyvalues', 'L20:M31');
dataA(1).d_core_i = xlsread(xlsfile, 'Onlyvalues', 'N20:O31');
dataA(1).d_core_o = xlsread(xlsfile, 'Onlyvalues', 'P20:Q31');
%% read and create surface area
surfdatafile = fullfile(indir, 'surfaceNucleus_24h_new.txt');
surfdata = load(surfdatafile);
dataA(1).surf = [surfdata(:,1)*60 surfdata(:,2:3)];
dataA(1).surf = [0 surfdata(1,2:3); dataA(1).surf];
% perform a spline fit to smooth the data
dataA(1).surfspl = surfSpline( dataA(1).surf(:,1), dataA(1).surf(:,2),7, 3, 8);
dataA(1).dsurfspl = fnder(dataA(1).surfspl, 1);
save(matfile, 'dataA');
end
end
end
matlabcode/delayedEquationModel/delayedMaturationCls.m
View file @ bddc56d1
classdef delayedMaturationCls < absDelayedMaturation
methods
function MO = delayedMaturationCls(force, showplot)
MO@absDelayedMaturation(force, showplot)
MO.dataF = MO.dataA;
% for i=1:2
% MO.protF(3-i).core = MO.protA(i).tot_core;
% MO.protF(3-i).noncore = MO.protA(i).tot_noncore;
% end
end
function so = solve(MO, par)
area = fnval(MO.dataF(1).surfspl,0);
so = ode45(@MO.sumPores, [0:1:200], [area*4;area*6] , odeset, par, MO.dataF(1).surfspl)
end
function dydt = sumPores(MO, t, y, par, surfspl)
area = fnval(surfspl,t);
dydt(1) = par(1)*(par(2)*area - y(1)-y(2))-par(3)*y(1);
dydt(2) = par(3)*y(1);
dydt = dydt';
end
function plotResult(MO,par)
so = solve(MO, par);
plot(so.x, [so.y(1,:)./fnval(MO.dataF(1).surfspl, so.x); so.y(2,:)./fnval(MO.dataF(1).surfspl, so.x)])
%plot(so.x, par(1)*(par(2)*fnval(MO.dataF(1).surfspl, so.x)-so.y)./fnval(MO.dataF(1).surfspl, so.x))
%plot(so.x, so.y)
end
end
classdef delayedMaturationCls < absDelayedMaturation
methods
function MO = delayedMaturationCls(force, showplot)
MO@absDelayedMaturation(force, showplot)
MO.dataF = MO.dataA;
% for i=1:2
% MO.protF(3-i).core = MO.protA(i).tot_core;
% MO.protF(3-i).noncore = MO.protA(i).tot_noncore;
% end
end
function so = solve(MO, par)
area = fnval(MO.dataF(1).surfspl,0);
so = ode45(@MO.sumPores, [0:1:200], [area*4;area*6] , odeset, par, MO.dataF(1).surfspl)
end
function dydt = sumPores(MO, t, y, par, surfspl)
area = fnval(surfspl,t);
dydt(1) = par(1)*(par(2)*area - y(1)-y(2))-par(3)*y(1);
dydt(2) = par(3)*y(1);
dydt = dydt';
end
function plotResult(MO,par)
so = solve(MO, par);
plot(so.x, [so.y(1,:)./fnval(MO.dataF(1).surfspl, so.x); so.y(2,:)./fnval(MO.dataF(1).surfspl, so.x)])
%plot(so.x, par(1)*(par(2)*fnval(MO.dataF(1).surfspl, so.x)-so.y)./fnval(MO.dataF(1).surfspl, so.x))
%plot(so.x, so.y)
end
end
end
\ No newline at end of file
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