Cant run this script, trying to plot a graph, please help

Can anyone tell me why the script below wont run??

I get this error when I attempt to run:

>> plot_data_AJ

Undefined function or variable 'PC3_DMSO_0p5uM_4c'.

Error in plot_data_AJ (line 12)

lplot(shift, PC3_DMSO_0p5uM_4c);title('PC3_DMSO_0p5uM_4c');

The script:

%% open folder with extracted data and import all extracted data (add a load line for each data set)
clear
cd('/Users/Ewan/Desktop/MATLAB/Extracted files')
load('PC3_DMSO_0p5uM_4c')
load('PC3_DMSO_0p5uM_5c')
load('PC3_DMSO_0p5uM_6c')
load('PNT2_DMSO_0p5uM_1')
load('PNT2_DMSO_0p5uM_3')
load('PNT2_DMSO_0p5uM_5')
%% quality control (run for each data set)
close all
lplot(shift, PC3_DMSO_0p5uM_4c);title('PC3_DMSO_0p5uM_4c'); 
[shift_cut PC3_DMSO_0p5uM_4c] = AJ_QT_cutrange(shift, PC3_DMSO_0p5uM_4c);
%% quality control (run for each data set)
close all
lplot(shift, PC3_DMSO_5uM_7);title('PC3_DMSO_0p5uM_5c'); 
[shift_cut PC3_DMSO_0p5uM_5c] = AJ_QT_cutrange(shift, PC3_DMSO_0p5uM_5c);
%% quality control (run for each data set)
close all
lplot(shift, PC3_DMSO_0p5uM_6c);title('PC3_DMSO_0p5uM_6c')
[shift_cut PC3_DMSO_0p5uM_6c] = AJ_QT_cutrange(shift, PC3_DMSO_0p5uM_6c);
%% quality control (run for each data set)
close all
lplot(shift, PNT2_DMSO_0p5uM_1);title('PNT2_DMSO_0p5uM_1')
[shift_cut PNT2_DMSO_0p5uM_1] = AJ_QT_cutrange(shift, PNT2_DMSO_0p5uM_1);
%% quality control (run for each data set)
close all
lplot(shift, PNT2_DMSO_0p5uM_3);title('PNT2_DMSO_0p5uM_3')
[shift_cut PNT2_DMSO_0p5uM_3] = AJ_QT_cutrange(shift, PNT2_DMSO_0p5uM_3);
%% quality control (run for each data set)
close all
lplot(shift, PNT2_DMSO_0p5uM_5);title('PNT2_DMSO_0p5uM_5')
[shift_cut PNT2_DMSO_0p5uM_5] = AJ_QT_cutrange(shift, PNT2_DMSO_0p5uM_5);
%% scale to 2935 peak
a=scale2935(PC3_DMSO_0p5uM_4c);
b=scale2935(PC3_DMSO_0p5uM_5c);
c=scale2935(PC3_DMSO_0p5uM_6c);
d=scale2935(PNT2_DMSO_0p5uM_1);
e=scale2935(PNT2_DMSO_0p5uM_3);
f=scale2935(PNT2_DMSO_0p5uM_5);
%% plot to compare data sets mean for each individual data set
Black = caz_rgb_chart('Black');
Magenta = caz_rgb_chart('Magenta');
Lime = caz_rgb_chart('Lime');
Red = caz_rgb_chart('Red');
Blue = caz_rgb_chart('Blue');
Purple = caz_rgb_chart('Purple');
 
figure;
h1= plot(shift_cut, mean(a), 'Color', [Black]);
set(h1, 'LineWidth',2);
hold on 
h2 = plot(shift_cut, mean(b), 'Color', [Black]);
set(h2, 'LineWidth',2);
h3 = plot(shift_cut, mean(c), 'Color', [Magenta]);
set(h3, 'LineWidth',2);
hold off
legend('PC3','PNT2');
set(legend,'Color','none');
axis('tight')
set(gca,'box','off')
set(gcf,'Color',[1 1 1])
xlabel('Raman Shift/cm^-^1','FontWeight','bold','FontSize',16,'FontName','Arial')
ylabel('Counts', 'FontWeight','bold','FontSize',16,'FontName','Arial')
set(gca,'FontWeight','bold','FontSize',16,'FontName','Arial');
%% group all data sets from same conditions together
PC3_all=[a;b;c];
PNT2_all=[d;e;f];
%% plot to compare data sets mean by condition
 
Black = caz_rgb_chart('Black');
Magenta = caz_rgb_chart('Magenta');
Lime = caz_rgb_chart('Lime');
Red = caz_rgb_chart('Red');
Blue = caz_rgb_chart('Blue');
Purple = caz_rgb_chart('Purple');
 
figure;
h1= plot(shift_cut, mean(PC3_all), 'Color', [Black]);
set(h1, 'LineWidth',1);
hold on 
h2 = plot(shift_cut, mean(PNT2_all), 'Color', [Magenta]);
set(h2, 'LineWidth',1);
hold off
legend('PC3','PNT2');
set(legend,'Color','none');
axis('tight')
set(gca,'box','off')
set(gcf,'Color',[1 1 1])
xlabel('Raman Shift/cm^-^1','FontWeight','bold','FontSize',16,'FontName','Arial')
ylabel('A.U.', 'FontWeight','bold','FontSize',16,'FontName','Arial')
set(gca,'FontWeight','bold','FontSize',16,'FontName','Arial');
%% ratio1 = 2850/2935
[ratio1_PC3]=extract_ratio_2850_2935_AJ(PC3_all);
[ratio1_PNT2]=extract_ratio_2850_2935_AJ(PNT2_all);
%% ratio2 = 2880/2935
[ratio2_PC3]=extract_ratio_2880_2935_AJ(PC3_all);
[ratio2_PNT2]=extract_ratio_2880_2935_AJ(PNT2_all);

Many thanks in advance

[Rik]

You are using load without the output parameter, which makes it very difficult to trace the source of errors and prevents m-lint from helping you out. I am also a bit confused why you are plotting data and immediately closing the figure again.

I suggest you load into a struct, convert this script into a function, and remove the clear. You might also find interesting and helpful hints on this page.

[Ewan Hislop]

The loaded files are .mat (extracted spc files). unfortunately what youre suggesting is beyond my matlab capability right now. I was hoping for a quick fix to the script that is already there. It was working for a friend sometime ago but he cant remember how exactly it ran.

Thanks for the suggestion though.

[Star Strider]

@Ewan — Rik’s suggestion is to do something like this:

D1 = load('PC3_DMSO_0p5uM_4c')

then post the result that appears in your Command Window. It will appear as structure ‘D1’ with at least one field. It may be that whatever is in that file is not named ‘PC3_DMSO_0p5uM_4c’. The same may be true for the other files.

Alternatively, you could attach all your .mat files to a comment here so we could look at them.

[Stephen23]

Ewan Hislop's "Answer" moved here:

Hi Star Strider,

I attempted the D1=, it created structures for each and I removed the clear but it failed at line 12 again.

Please find attached the .mat files. I hope you can make more sense out of this as I'm out of ideas.

Thanks again :)

Answer 1

[Star Strider]

My pleasure.

When I did:

D1 = load('PC3_DMSO_0.5uM_4c.mat')

I got:

D1 = 

  struct with fields:

    PC3_TOFA_5uM_8: [296×633 double]
            output: [425376×1 double]
            ratio1: [21×32 double]
            ratio2: [21×32 double]
             shift: [633×1 double]

I am not certain which one of those you want. It is important t note that none of them is named ‘PC3_DMSO_0p5uM_4c’.

Also, the file names in your code do not match the file names you attached. The actual file names have decimal points, while the file names in your code have the letter ‘p’ in that position.

I did not download the other files. The one I downloaded and opened illustrates the problem.

We cannot run your code, because we do not have the ‘lplot’ function. However, you may not need it, because this:

D1 = load('PC3_DMSO_0.5uM_4c.mat')
PC3_TOFA_5uM_8 = D1.PC3_TOFA_5uM_8;
shift = D1.shift;

figure
plot(shift, PC3_TOFA_5uM_8)
grid

may do what you want. (I have no idea what I’m looking at, in that plot, so I cannot comment further.)

[Ewan Hislop]

Hi Star strider,

Firstly thanks so much for taking a look at this.

Hmmm there seems to be alot of mismatching in the code.

I do have the lplot function in my matlab folder if this is of any use?

I will persist with this, where tere is a will there is a way :)

Best,

Ewan

[Star Strider]

Ewan Hislop’s Answer moved here:

Basically what Im trying to achieve with this script is the average spectrum of PC3 (3files) vs PNT2 cells (3files).

Any functions that are not listed i the script I do have.

Although I uploaded a 0.5uM files I had changed this in my matlab extracted files to match the script ie 0p5.

The code you gave me Star gave me the spectrum for that file only.

Sorry for being a nuisance.

Any ideas?

[Star Strider]

You’re not a nuisance. I just have no idea what you are doing, or what the data in your files are.

You should have all the MATLAB functions I use in my Answer and Comments.

To process your files, see for example: Import or Export a Sequence of Files (link).

[Image Analyst]

Well sometimes he is, like when he deletes his questions, as he's done before. Below is the original question here:

Can anyone tell me why the script below wont run??

I get this error when I attempt to run:

>> plot_data_AJ

Undefined function or variable 'PC3_DMSO_0p5uM_4c'.

Error in plot_data_AJ (line 12)

lplot(shift, PC3_DMSO_0p5uM_4c);title('PC3_DMSO_0p5uM_4c');

The script:

%% open folder with extracted data and import all extracted data (add a load line for each data set)
clear
cd('/Users/Ewan/Desktop/MATLAB/Extracted files')
load('PC3_DMSO_0p5uM_4c')
load('PC3_DMSO_0p5uM_5c')
load('PC3_DMSO_0p5uM_6c')
load('PNT2_DMSO_0p5uM_1')
load('PNT2_DMSO_0p5uM_3')
load('PNT2_DMSO_0p5uM_5')
%% quality control (run for each data set)
close all
lplot(shift, PC3_DMSO_0p5uM_4c);title('PC3_DMSO_0p5uM_4c'); 
[shift_cut PC3_DMSO_0p5uM_4c] = AJ_QT_cutrange(shift, PC3_DMSO_0p5uM_4c);
%% quality control (run for each data set)
close all
lplot(shift, PC3_DMSO_5uM_7);title('PC3_DMSO_0p5uM_5c'); 
[shift_cut PC3_DMSO_0p5uM_5c] = AJ_QT_cutrange(shift, PC3_DMSO_0p5uM_5c);
%% quality control (run for each data set)
close all
lplot(shift, PC3_DMSO_0p5uM_6c);title('PC3_DMSO_0p5uM_6c')
[shift_cut PC3_DMSO_0p5uM_6c] = AJ_QT_cutrange(shift, PC3_DMSO_0p5uM_6c);
%% quality control (run for each data set)
close all
lplot(shift, PNT2_DMSO_0p5uM_1);title('PNT2_DMSO_0p5uM_1')
[shift_cut PNT2_DMSO_0p5uM_1] = AJ_QT_cutrange(shift, PNT2_DMSO_0p5uM_1);
%% quality control (run for each data set)
close all
lplot(shift, PNT2_DMSO_0p5uM_3);title('PNT2_DMSO_0p5uM_3')
[shift_cut PNT2_DMSO_0p5uM_3] = AJ_QT_cutrange(shift, PNT2_DMSO_0p5uM_3);
%% quality control (run for each data set)
close all
lplot(shift, PNT2_DMSO_0p5uM_5);title('PNT2_DMSO_0p5uM_5')
[shift_cut PNT2_DMSO_0p5uM_5] = AJ_QT_cutrange(shift, PNT2_DMSO_0p5uM_5);
%% scale to 2935 peak
a=scale2935(PC3_DMSO_0p5uM_4c);
b=scale2935(PC3_DMSO_0p5uM_5c);
c=scale2935(PC3_DMSO_0p5uM_6c);
d=scale2935(PNT2_DMSO_0p5uM_1);
e=scale2935(PNT2_DMSO_0p5uM_3);
f=scale2935(PNT2_DMSO_0p5uM_5);
%% plot to compare data sets mean for each individual data set
Black = caz_rgb_chart('Black');
Magenta = caz_rgb_chart('Magenta');
Lime = caz_rgb_chart('Lime');
Red = caz_rgb_chart('Red');
Blue = caz_rgb_chart('Blue');
Purple = caz_rgb_chart('Purple');
 
figure;
h1= plot(shift_cut, mean(a), 'Color', [Black]);
set(h1, 'LineWidth',2);
hold on 
h2 = plot(shift_cut, mean(b), 'Color', [Black]);
set(h2, 'LineWidth',2);
h3 = plot(shift_cut, mean(c), 'Color', [Magenta]);
set(h3, 'LineWidth',2);
hold off
legend('PC3','PNT2');
set(legend,'Color','none');
axis('tight')
set(gca,'box','off')
set(gcf,'Color',[1 1 1])
xlabel('Raman Shift/cm^-^1','FontWeight','bold','FontSize',16,'FontName','Arial')
ylabel('Counts', 'FontWeight','bold','FontSize',16,'FontName','Arial')
set(gca,'FontWeight','bold','FontSize',16,'FontName','Arial');
%% group all data sets from same conditions together
PC3_all=[a;b;c];
PNT2_all=[d;e;f];
%% plot to compare data sets mean by condition
 
Black = caz_rgb_chart('Black');
Magenta = caz_rgb_chart('Magenta');
Lime = caz_rgb_chart('Lime');
Red = caz_rgb_chart('Red');
Blue = caz_rgb_chart('Blue');
Purple = caz_rgb_chart('Purple');
 
figure;
h1= plot(shift_cut, mean(PC3_all), 'Color', [Black]);
set(h1, 'LineWidth',1);
hold on 
h2 = plot(shift_cut, mean(PNT2_all), 'Color', [Magenta]);
set(h2, 'LineWidth',1);
hold off
legend('PC3','PNT2');
set(legend,'Color','none');
axis('tight')
set(gca,'box','off')
set(gcf,'Color',[1 1 1])
xlabel('Raman Shift/cm^-^1','FontWeight','bold','FontSize',16,'FontName','Arial')
ylabel('A.U.', 'FontWeight','bold','FontSize',16,'FontName','Arial')
set(gca,'FontWeight','bold','FontSize',16,'FontName','Arial');
%% ratio1 = 2850/2935
[ratio1_PC3]=extract_ratio_2850_2935_AJ(PC3_all);
[ratio1_PNT2]=extract_ratio_2850_2935_AJ(PNT2_all);
%% ratio2 = 2880/2935
[ratio2_PC3]=extract_ratio_2880_2935_AJ(PC3_all);
[ratio2_PNT2]=extract_ratio_2880_2935_AJ(PNT2_all);

Many thanks in advance