Bioinformatics Toolbox™

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

Syntax

msdotplot(Peaks, Times) msdotplot(FigHandle, Peaks, Times) msdotplot(..., 'Quantile', QuantileValue) PlotHandle = msdotplot(...)

Arguments

Peaks

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. Each element corresponds to a spectrum or retention time.

Tip You can use the mzxml2peaks function to create the Peaks cell array.

Times

Vector of retention times associated with an LC/MS or GC/MS data set. The number of elements in Times equals the number of elements in the cell array Peaks.

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

FigHandle Handle to an open Figure window such as one created by the msheatmap function.

QuantileValue Value that specifies a percentage. When peaks are ranked by intensity, only those that rank above this percentage are plotted. Choices are any value ≥ 0 and ≤ 1. Default is 0. For example, setting QuantileValue = 0 plots all peaks, and setting QuantileValue = 0.8 plots only the 20% most intense peaks.

Return Values

PlotHandle Handle to the line series object (figure plot).

Description

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

Tip 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. Choices are any value ≥ 0 and ≤ 1. Default is 0. For example, setting QuantileValue = 0 plots all peaks, and setting QuantileValue = 0.8 plots only the 20% most intense peaks.

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

Load a MAT-file, included with the Bioinformatics Toolbox software, which contains LC/MS data variables, including peaks and ret_time. 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(peaks,ret_time,'Quantile',0.95)
```

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

[MZ,Y] = msppresample(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(peaks,ret_time)
axis([480 532 375 485])
```