msdotplot

Plot set of peak lists from LC/MS or GC/MS data set

Syntax

msdotplot(Peaklist,Times)

msdotplot(FigHandle,Peaklist, Times)

msdotplot(___,Quantile=QuantileValue)

PlotHandle = msdotplot(___)

Description

msdotplot(Peaklist,Times) plots a set of peak lists from a liquid chromatography/mass spectrometry (LC/MS) or gas chromatography/mass spectrometry (GC/MS) data set represented by Peaklist, a cell array of peak lists, where each element is a two-column matrix with m/z values in the first column and ion intensity values in the second column, and Times, a vector of retention times associated with the spectra. Peaklist and Times have the same number of elements. The data is plotted into any existing figure generated by the msheatmap function. Otherwise, the data is plotted into a new Figure window.

msdotplot(FigHandle,Peaklist, Times) plots the set of peak lists into the axes contained in an open Figure window with the handle FigHandle.

This syntax is useful to overlay a dot plot on top of a heat map of mass spectrometry data created with the msheatmap function.

msdotplot(___,Quantile=QuantileValue) plots only the most intense peaks, specifically those in the percentage above the specified QuantileValue.

PlotHandle = msdotplot(___) returns a handle to the line series object (figure plot). You can use this handle as input to the get function to display a list of the plot's properties. You can use this handle as input to the set function to change the plot's properties, including showing and hiding points.

Examples

Plot Set of Peak Lists and Heat Map of LC/MS Data

Load a MAT-file, included with the Bioinformatics Toolbox™ software, which contains LC/MS data variables, including ms_peaks and ret_time.

• ms_peaks is a cell array of peak lists, where each element is a two-column matrix of m/z values and ion intensity values, and each element corresponds to a spectrum or retention time.

• ret_time is a column vector of retention times associated with the LC/MS data set.

load lcmsdata 

Create a dot plot with only the 5% most intense peaks.

msdotplot(ms_peaks,ret_time,Quantile=0.95)

Resample the data, then create a heat map of the LC/MS data.

[MZ,Y] = msppresample(ms_peaks,5000);
msheatmap(MZ,ret_time,log(Y))

Overlay the dot plot on the heat map, and then zoom in to see the detail.

msdotplot(ms_peaks,ret_time)
axis([480 532 375 485])

Input Arguments

Peaklist — Peak lists

cell array

Peak lists, specified as a cell array where each element is a two-column matrix with m/z values in the first column and ion intensity values in the second column. Each element corresponds to a spectrum or retention time.

You can use the mzxml2peaks function to create Peaklist.

Data Types: cell

Times — Retention times associated with LC/MS or GC/MS data set

vector

Retention times associated with an LC/MS or GC/MS data set, specified as a vector. The number of elements in Times equals the number of elements in the cell array Peaklist.

You can use the mzxml2peaks function to create the Times vector.

Data Types: double

FigHandle — Handle to open Figure window

graphics object handle

Handle to an open Figure window, specified as graphics object handle.

QuantileValue — Percentage

0 (default) | number in the range [0 1]

Percentage, specified as a number between 0 and 1 (including 0 and 1). Setting this value to 0 plots all peaks, and setting QuantileValue to 0.8 plots only the 20% most intense peaks.

Data Types: double

Output Arguments

PlotHandle — Handle to line series object (figure plot)

graphics object handle

Handle to the line series object (figure plot), returned as a graphics object handle.

Version History

Introduced in R2007a