getting error in code when running

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Ehtisham
Ehtisham 2024-1-22
评论： Harald 2024-1-23
Ran in:
CheckKFmax_1()
R*peak: 65.4697 T-peak: 4.5 50% form peak to ss : 57.7799 R* Steady state: 50.0901 T-50 : 53 R*peak/R*ss: 1.307 Δ (R*peak-R*ss) : 15.3795 R*peak: 63.795 T-peak: 3.7 50% form peak to ss : 48.6249 R* Steady state: 33.4548 T-50 : 39.1 R*peak/R*ss: 1.9069 Δ (R*peak-R*ss) : 30.3402 R*peak: 62.4078 T-peak: 3.2 50% form peak to ss : 43.7608 R* Steady state: 25.1139 T-50 : 31.3 R*peak/R*ss: 2.485 Δ (R*peak-R*ss) : 37.2938 R*peak: 61.2429 T-peak: 2.9 50% form peak to ss : 40.6736 R* Steady state: 20.1044 T-50 : 26.2 R*peak/R*ss: 3.0462 Δ (R*peak-R*ss) : 41.1385 R*peak: 60.17 T-peak: 2.7 50% form peak to ss : 38.4641 R* Steady state: 16.7582 T-50 : 22.6 R*peak/R*ss: 3.5905 Δ (R*peak-R*ss) : 43.4118 R*peak: 79.1276 T-peak: 4.7 50% form peak to ss : 72.9374 R* Steady state: 66.7472 T-50 : 56.7 R*peak/R*ss: 1.1855 Δ (R*peak-R*ss) : 12.3804 R*peak: 77.8834 T-peak: 3.7 50% form peak to ss : 64.0101 R* Steady state: 50.1368 T-50 : 46.4 R*peak/R*ss: 1.5534 Δ (R*peak-R*ss) : 27.7466 R*peak: 76.843 T-peak: 3.2 50% form peak to ss : 58.5003 R* Steady state: 40.1576 T-50 : 39.4 R*peak/R*ss: 1.9135 Δ (R*peak-R*ss) : 36.6854 R*peak: 75.9321 T-peak: 3 50% form peak to ss : 54.7034 R* Steady state: 33.4747 T-50 : 34 R*peak/R*ss: 2.2683 Δ (R*peak-R*ss) : 42.4574 R*peak: 75.0963 T-peak: 2.8 50% form peak to ss : 51.9009 R* Steady state: 28.7056 T-50 : 30.1 R*peak/R*ss: 2.6161 Δ (R*peak-R*ss) : 46.3908 R*peak: 85.0465 T-peak: 4.7 50% form peak to ss : 80.0572 R* Steady state: 75.0679 T-50 : 58.7 R*peak/R*ss: 1.1329 Δ (R*peak-R*ss) : 9.9786 R*peak: 84.0739 T-peak: 3.6 50% form peak to ss : 72.099 R* Steady state: 60.1241 T-50 : 50.8 R*peak/R*ss: 1.3983 Δ (R*peak-R*ss) : 23.9498 R*peak: 83.2706 T-peak: 3.2 50% form peak to ss : 66.7106 R* Steady state: 50.1506 T-50 : 44.5 R*peak/R*ss: 1.6604 Δ (R*peak-R*ss) : 33.12 R*peak: 82.5506 T-peak: 2.9 50% form peak to ss : 62.7819 R* Steady state: 43.0133 T-50 : 39.7 R*peak/R*ss: 1.9192 Δ (R*peak-R*ss) : 39.5374 R*peak: 81.889 T-peak: 2.7 50% form peak to ss : 59.7715 R* Steady state: 37.6539 T-50 : 35.7 R*peak/R*ss: 2.1748 Δ (R*peak-R*ss) : 44.2351 R*peak: 88.3479 T-peak: 4.7 50% form peak to ss : 84.2016 R* Steady state: 80.0553 T-50 : 60.2 R*peak/R*ss: 1.1036 Δ (R*peak-R*ss) : 8.2926 R*peak: 87.5604 T-peak: 3.8 50% form peak to ss : 77.1745 R* Steady state: 66.7885 T-50 : 53.1 R*peak/R*ss: 1.311 Δ (R*peak-R*ss) : 20.772 R*peak: 86.9035 T-peak: 3.2 50% form peak to ss : 72.0973 R* Steady state: 57.291 T-50 : 47.9 R*peak/R*ss: 1.5169 Δ (R*peak-R*ss) : 29.6124 R*peak: 86.3115 T-peak: 3 50% form peak to ss : 68.2354 R* Steady state: 50.1594 T-50 : 43.3 R*peak/R*ss: 1.7207 Δ (R*peak-R*ss) : 36.1521 R*peak: 85.7664 T-peak: 2.7 50% form peak to ss : 65.1864 R* Steady state: 44.6064 T-50 : 39.8 R*peak/R*ss: 1.9227 Δ (R*peak-R*ss) : 41.16 R*peak: 90.4558 T-peak: 4.6 50% form peak to ss : 86.9198 R* Steady state: 83.3838 T-50 : 61.4 R*peak/R*ss: 1.0848 Δ (R*peak-R*ss) : 7.072 R*peak: 89.7938 T-peak: 3.8 50% form peak to ss : 80.6666 R* Steady state: 71.5394 T-50 : 55 R*peak/R*ss: 1.2552 Δ (R*peak-R*ss) : 18.2545 R*peak: 89.2374 T-peak: 3.3 50% form peak to ss : 75.9399 R* Steady state: 62.6424 T-50 : 50.3 R*peak/R*ss: 1.4246 Δ (R*peak-R*ss) : 26.595 R*peak: 88.7405 T-peak: 2.9 50% form peak to ss : 72.2258 R* Steady state: 55.711 T-50 : 46.4 R*peak/R*ss: 1.5929 Δ (R*peak-R*ss) : 33.0294 R*peak: 88.2778 T-peak: 2.7 50% form peak to ss : 69.2131 R* Steady state: 50.1483 T-50 : 42.9 R*peak/R*ss: 1.7603 Δ (R*peak-R*ss) : 38.1295
Error using .
Unrecognized table variable name 'Kf1Max'.

Error in solution>CheckKFmax_1 (line 86)
Kf1Max_values = unique(combined_table.Kf1Max);
function CheckKFmax_1()
% Parameters
timespan = 0:0.1:500; % Time vector
Receptor_concentration = 100; % Concentration of Receptor
% Initial conditions
C_LigandReceptor_0 = 0; % Initial concentration of the ligand-receptor complex
% Define different ranges of Kf1Max values
Kf1Max_values = [20, 40, 60, 80, 100];
Kb1Max_values = [20, 40, 60, 80, 100];
% Create a cell array to store tables for different Kf1Max and Kb1Max ranges
tables_cell = cell(length(Kf1Max_values), length(Kb1Max_values));
for i = 1:length(Kf1Max_values)
Kf1Max = Kf1Max_values(i);
for j = 1:length(Kb1Max_values)
Kb1Max = Kb1Max_values(j);
% Time-dependent forward reaction rate constants
t_start = 5; % Start time of receptor pulse
t_end = 500; % Duration of receptor pulse
Kf1Min = 1;
Kf1Tau_on = -1;
Kf1Tau_off = -1;
% Time-dependent backward reaction rate constants
Kb1Min = 10;
Kb1Tau_on = -0.01;
Kb1Tau_off = -0.01;
% Define anonymous functions for forward and backward reaction rates
kf_1 = @(t) calculate_kf(t, t_start, t_end, Kf1Max, Kf1Min, Kf1Tau_on, Kf1Tau_off);
kb_1 = @(t) calculate_kb(t, t_start, t_end, Kb1Max, Kb1Min, Kb1Tau_on, Kb1Tau_off);
% Solve the ODE system
[t, y] = ode45(@(t, y) ode_LR(t, y, kf_1, kb_1), timespan, [Receptor_concentration; C_LigandReceptor_0]);
% Extract the concentrations
receptor_concentration = y(:, 1);
ligand_Receptor_concentration = y(:, 2);
% Displaying the peak value and its corresponding time
[peak_value, peak_time_idx] = max(ligand_Receptor_concentration);
time_to_peak = t(peak_time_idx);
% Calculate the time between start and peak time
time_to_peak = time_to_peak - t_start;
% Find steady state and time to approach 50% of the steady state
steady_state = mean(ligand_Receptor_concentration(end-50:end)); % Considering the last few points for steady state
% Calculate T-50: Time to reach 50% of the peak value
half_peak_value = (steady_state + peak_value)/2;
% Find the indices where the ligand receptor concentration is closest to half the peak value
[~, idx_50_percent] = min(abs(ligand_Receptor_concentration(peak_time_idx:end) - half_peak_value));
% Get the time corresponding to the closest index
time_to_50_percent = t(idx_50_percent)- time_to_peak;
% Find the ratio of the R*peak/R* steady state
peak_to_steady_state_ratio = peak_value / steady_state;
% Find the ratio of the R*peak/R* steady state
Delta = peak_value - steady_state;
disp(['R*peak: ', num2str(peak_value)]);
disp(['T-peak: ', num2str(time_to_peak)]);
disp(['50% form peak to ss : ', num2str(half_peak_value)]);
disp(['R* Steady state: ', num2str(steady_state)]);
disp(['T-50 : ', num2str(time_to_50_percent)]);
disp(['R*peak/R*ss: ', num2str(peak_to_steady_state_ratio)]);
disp(['Δ (R*peak-R*ss) : ', num2str(Delta)]);
R_peak_values(i) = peak_value;
T_peak_values(i) = time_to_peak;
R_steady_state_values(i) = steady_state;
T_50_values(i) = time_to_50_percent;
R_peak_R_ss_values(i) = peak_to_steady_state_ratio;
Delta_values(i) = Delta;
% Create a table to combine all results
data_table = table(R_peak_values', T_peak_values', R_steady_state_values', T_50_values', R_peak_R_ss_values', Delta_values', ...
'VariableNames', {'R_peak', 'T_peak', 'R_steady_state', 'T_50', 'R_peak_R_ss', 'Delta'});
% Store the table in the cell array for each Kf1Max range
tables_cell{i, j} = data_table;
% Generate a unique filename for each combination of Kf1Max and Kb1Max values
csv_filename = sprintf('interaction_data_Kf1Max_%d_Kb1Max_%d.csv', Kf1Max, Kb1Max);
writetable(data_table, csv_filename);
end
end
% Combine all results into a single table
combined_table = vertcat(tables_cell{:});
% Generate a unique filename for the combined table
combined_csv_filename = 'combined_interaction_data_all.csv';
writetable(combined_table, combined_csv_filename);
% Load the combined interaction data CSV file
combined_csv_filename = 'combined_interaction_data_all.csv';
combined_table = readtable(combined_csv_filename);
% Extract Kf1Max and Kb1Max values from the combined table
Kf1Max_values = unique(combined_table.Kf1Max);
Kb1Max_values = unique(combined_table.Kb1Max);
% Initialize matrices to store Kf1Max, Kb1Max, and R*peak values
Kf1Max_matrix = zeros(length(Kb1Max_values), length(Kf1Max_values));
Kb1Max_matrix = zeros(length(Kb1Max_values), length(Kf1Max_values));
R_peak_matrix = zeros(length(Kb1Max_values), length(Kf1Max_values));
% Populate matrices with values from the combined table
for i = 1:length(Kf1Max_values)
for j = 1:length(Kb1Max_values)
idx = find(combined_table.Kf1Max == Kf1Max_values(i) & combined_table.Kb1Max == Kb1Max_values(j));
if ~isempty(idx)
Kf1Max_matrix(j, i) = Kf1Max_values(i);
Kb1Max_matrix(j, i) = Kb1Max_values(j);
R_peak_matrix(j, i) = combined_table.R_peak(idx);
end
end
end
% Create a 3D fsurf plot
figure;
fsurf(Kf1Max_matrix, Kb1Max_matrix, R_peak_matrix);
xlabel('Kf1Max');
ylabel('Kb1Max');
zlabel('R*peak');
title('3D fsurf Plot for Combined R*peak Values');
end
function kf_1 = calculate_kf(t, t_start, t_end, Kf1Max, Kf1Min, Kf1Tau_on, Kf1Tau_off)
% Initialize kf_1
kf_1 = zeros(size(t));
% Initial phase: Constant value Kf1Min
initial_phase = t < t_start;
kf_1(initial_phase) = Kf1Min;
% Increasing phase: Exponential growth from Kf1Min to Kf1Max
increasing_phase = t >= t_start & t < t_end;
kf_1(increasing_phase) = Kf1Max - (Kf1Max - Kf1Min) * exp(Kf1Tau_on * (t(increasing_phase) - t_start));
% Decreasing phase: Exponential decay from Kf1Max to Kf1Min
kf_end = Kf1Max - (Kf1Max - Kf1Min) * exp(Kf1Tau_on * (t_end - t_start));
decreasing_phase = t >= t_end;
kf_1(decreasing_phase) = Kf1Min + (kf_end - Kf1Min) * exp(Kf1Tau_off * (t(decreasing_phase) - t_end));
end
function kb_1 = calculate_kb(t, t_start, t_end, Kb1Max, Kb1Min, Kb1Tau_on, Kb1Tau_off)
% Initialize kb_1
kb_1 = zeros(size(t));
% Initial phase: Constant value Kb1Min
initial_phase = t < t_start;
kb_1(initial_phase) = Kb1Min;
% Increasing phase: Exponential growth from Kb1Min to Kb1Max
increasing_phase = t >= t_start & t < t_end;
kb_1(increasing_phase) = Kb1Max - (Kb1Max - Kb1Min) * exp(Kb1Tau_on * (t(increasing_phase) - t_start));
% Decreasing phase: Exponential decay from Kb1Max to Kb1Min
kb_end = Kb1Max - (Kb1Max - Kb1Min) * exp(Kb1Tau_on * (t_end - t_start));
decreasing_phase = t >= t_end;
kb_1(decreasing_phase) = Kb1Min + (kb_end - Kb1Min) * exp(Kb1Tau_off * (t(decreasing_phase) - t_end));
end
function dydt = ode_LR(t, y, kf_1, kb_1)
% Unpack the concentrations
Receptor_concentration = y(1);
C_LigandReceptor = y(2);
% Define the ODE system
dReceptor_dt = -kf_1(t) * Receptor_concentration + kb_1(t) * C_LigandReceptor;
d_CLigandReceptor_dt = kf_1(t) * Receptor_concentration - kb_1(t) * C_LigandReceptor;
% Pack the derivatives into a column vector
dydt = [dReceptor_dt; d_CLigandReceptor_dt];
end

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回答（1 个）

Harald
Harald 2024-1-22
Hi,
after running your code, combined_table does not contain anything called Kf1Max or even remotely similar to it.
Best wishes,
Harald
  3 个评论
显示 1更早的评论
Image Analyst
Image Analyst 2024-1-23
OK, fine - the values are already there in the table. It looks like Kf1Max is not even involved. Do you have an (x,y) coordinate for each value of R_peak? If so, then use surf
Harald
Harald 2024-1-23
@Ehtisham, it is of course always good to know where you ultimately want to go. However, I don't think this resolves the imminent problem: you are trying to extract a variable from a table that isn't there.
So, as Image Analyst suggests, you will need to obtain that variable from "somewhere" else.

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