Peak labeling on spectroscopic data using plotjdx function

I am plotting some Raman spectroscopy data, using the plotjdx function created by Micke Malmstrom (here; requires the Bioinformatics Toolbox). This works great, but I would like to find and label the peaks, and cannot figure out where in the script I should do this. My sense is that I need to use the findpeaks function built into MATLAB, but I have yet to incorporate it successfully. Do you have advice on where I could insert the "findpeaks" function and related lines of code?

Here is the plotjdx function. I have attached a test spectra file.

function h=plotjdx(variable,h)
% h=plotjdx(variable,h) Plots a (selection of) jdx file(s) in a new or 
% specified figure. If no file is specified then the function ask for user
% to select files...
%
% input 'variable' can be: 
% - a 'filename' of a jdx file, 
% - a cell with filenames to several jdx files or
% - JCAMPStruct to be plotted in
%
% input figure handle 'h' is optional
%
% BSD [e-mail]
% Version 2014-12-18


if nargin==0
    % If no input, ask for files
    [filename,folderpath] = uigetfile({'*.*'},...
        'Select the .jdx files to plot','MultiSelect','on');
    
    % see if handle to fig is specified
    if exist('h','var')
        h=figure(h);clf, hold on
    else % make new figure
        h=figure;clf, hold on
    end
    
    if iscell(filename)
        %its several files
        files=filename;
        
        % now plot all files in same figure h
        for ii=1:length(filename)
            h=plotjdx([folderpath files{ii}],h);
        end
        legend show
        return
    else %is only one file so plot it
        h=plotjdx([folderpath filename],h);
        return
    end
    
% if the input is characters then 'variable' is a filename
elseif ischar(variable)
    %import and plot the file
    variable=jcampread(variable);
    h=plotjdx(variable);
    
% if the input is a cell then 'variable' is a bunch of filenames    
elseif iscell(variable)
    
    % see if handle to fig is specified
    if exist('h','var')
        h=figure(h);clf, hold on
    else % make new figure
        h=figure;clf, hold on
    end
            % now plot all files in same figure h
    for ii=1:length(variable)
        h=plotjdx([variable{ii}],h);
    end
    legend show
    
    return
    
 % if the input is a structure then 'variable' is the actual JCAMPStruct
elseif isstruct(variable)
    data = variable.Blocks(1);
    h=plot(data.XData,data.YData, 'DisplayName',variable.Title);
    
    xlabel(data.XUnits);
    ylabel(data.YUnits);
end

[Mathieu NOE]

hello

sure you need findpeaks

there is an example in the documentation for how to plot the peaks

that must be inserted after the plot command , for example in the last section of your code :

 % if the input is a structure then 'variable' is the actual JCAMPStruct
elseif isstruct(variable)
    data = variable.Blocks(1);
    h=plot(data.XData,data.YData, 'DisplayName',variable.Title);
    
    xlabel(data.XUnits);
    ylabel(data.YUnits);
end

now, beside that I am a bit surprised to see that this function (plotjdx) call itself in the script

very surprising !!!

[Natalie Raia]

Great, thank you. Yes- I think that is what threw me off a bit in trying to understand how everything was working!

Answer 1

[Tarunbir Gambhir]

You can use the findpeaks function in the last section of the script when you get the X and Y data.

You can try the following:

% if the input is a structure then 'variable' is the actual JCAMPStruct
elseif isstruct(variable)
    data = variable.Blocks(1);
    h=plot(data.XData,data.YData, 'DisplayName',variable.Title);
    findpeaks(data.YData,data.XData,'NPeaks',5,'SortStr','descend');
    
    xlabel(data.XUnits);
    ylabel(data.YUnits);
    end

Using the above configurations for "findpeaks", you will get the top 5 peaks labeled in the figure.

Alternatively, if you do not want a labeled figure and rather get the peak values and locations, you can provide output while calling the function.

[pk,loc] = findpeaks(data.YData,data.XData,'NPeaks',5,'SortStr','descend');

The peak values and locations will be output in the variables "pk" and "loc" respectively.

For further customization on finding the peaks using this fuction, refer the Mathworks Documentation here.

[Natalie Raia]

Thank you- I got it to work! Now I will read the Mathworks Documentation further to get it to also plot the x-axis value of each of the peaks.