mairplot

Create intensity versus ratio scatter plot of microarray data

Syntax

mairplot(DataX,DataY)

[Intensity,Ratio] = mairplot(DataX,DataY)

[Intensity,Ratio,H] = mairplot(DataX,DataY)

___ = mairplot(DataX,DataY,Name=Value)

Description

mairplot(DataX,DataY) creates a scatter plot that plots log₁₀ of the product of the DataX and DataY intensities versus log₂ of the intensity ratios.

[Intensity,Ratio] = mairplot(DataX,DataY) returns the intensity and ratio values. If you set Normalize to true, the returned ratio values are normalized.

[Intensity,Ratio,H] = mairplot(DataX,DataY) returns the handle to the plot. Use H to modify the plot after it is created.

___ = mairplot(DataX,DataY,Name=Value) specifies additional options using one or more name-value arguments. Use any arguments from the previous syntaxes.

Examples

Create Intensity Versus Ratio Scatter Plot

Load a sample GPR file containing microarray data.

maStruct = gprread("mouse_a1wt.gpr");

Extract the green (cy3) and red (cy5) signals from the data.

cy5data = magetfield(maStruct,"F635 Median");
cy3data = magetfield(maStruct,"F532 Median");

Create an intensity versus ratio scatter plot of the cy3 and cy5 data. Normalize the data and add a title and labels.

mairplot(cy5data,cy3data,Normalize=true, ...
         Title="Normalized R vs G IR plot", ...
         Labels=maStruct.Names);

Create a normalized microarrray plot of the cy3 and cy5 data without the user interface components.

mairplot(cy5data,cy3data,Normalize=true,Type="MA",PlotOnly=true);

The intensity versus ratio scatter plot displays the following:

• $$lo{g}_{10}$$ (Intensity) versus $$lo{g}_2$$ (Ratio) scatter plot of genes.

• Two horizontal fold change lines at a fold change level of 2, which corresponds to a ratio of 1 and –1 on a log 2 (Ratio) scale. Lines will be at different fold change levels, if you used the FactorLines argument.

• Data points for genes that are considered differentially expressed (outside of the fold change lines) appear in orange.

After you display the intensity versus ratio scatter plot, you can interactively do the following:

• Adjust the horizontal fold change lines by click-dragging one line or entering a value in the Fold Change text box, then clicking Update.

• Display labels for data points by clicking a data point.

• Select a gene from the Up Regulated or Down Regulated list to highlight the corresponding data point in the plot. Press and hold Ctrl or Shift to select multiple genes.

• Zoom the plot by selecting Tools > Zoom In or Tools > Zoom Out.

• View lists of significantly up-regulated and down-regulated genes, and optionally, export the gene labels and indices to a structure in the MATLAB® Workspace by clicking Export.

• Normalize the data by clicking the Normalize button, then selecting whether to show the normalized plot in a separate window. If you show the normalized plot in a separate window, the Show smooth curve check box becomes available in the original (unnormalized) plot.

To select different lowess normalization options before normalizing, select Tools > Set LOWESS Normalization Options, then enter options in the Options for LOWESS dialog box.

Input Arguments

DataX — Intensity values

DataMatrix object | vector

Intensity values, specified as a DataMatrix object or vector of gene expression values where each row corresponds to a gene. For example, in a two-color microarray experiment, DataX can be cy3 intensity values and DataY can be cy5 intensity values.

DataY — Intensity values

DataMatrix object | vector

Intensity values, specified as a DataMatrix object or vector of gene expression values where each row corresponds to a gene. For example, in a two-color microarray experiment, DataX can be cy3 intensity values and DataY can be cy5 intensity values.

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: Normalize=true,Type="MA",PlotOnly=true

Type — Plot type

"IR" (default) | "MA"

Plot type, specified as "IR" or "MA".

• "IR" plots log₁₀ of the product of the DataX and DataY intensities versus log₂ of the intensity ratios.

• "MA" plots (1/2)log₂ of the product of the DataX and DataY intensities versus log₂ of the intensity ratios.

Data Types: char | string

LogTrans — Controls for conversion of data from natural to log ₂ scale

true (default) | false

Controls for conversion of data in DataX and DataY from natural to log ₂ scale, specified as true or false. Set the value to false, when the data is already log₂ scale. The default valuetrue assumes the data is natural scale.

Data Types: logical

FactorLines — Control to add lines to plot showing factor of N change

2 (default) | number

Control to add lines to the plot showing a factor of N change, specified as a number. The default value 2 corresponds to a level of 1 and -1 on a log₂ scale.

Tip

You can also change the factor lines interactively, after creating the plot.

Data Types: double

Title — Plot title

string | character vector

Plot title, specified as a string or character vector.

Data Types: char | string

Labels — Labels for data

string vector | cell array of character vectors

Labels for the data, specified as a string vector or cell array of character vectors. If labels are defined, then clicking a point on the plot shows the label corresponding to that point.

Data Types: string | cell

Normalize — Control for displaying lowess normalized ratio values

false (default) | true

Control for displaying lowess normalized ratio values, specified as true or false. If this value is set to true, the mairplot function displays lowess normalized ratio values.

Tip

You can also normalize the data from the MAIR Plot window, after creating the plot.

Data Types: logical

LowessOptions — Lowess normalization options

cell array

Lowess normalization options, specified as a cell array of one, two, or three of these name-value pair arguments: Order, Robust, Span. For more information on the name-value pair arguments, see malowess.

Data Types: cell

Showplot — Control for displaying scatter plot

true (default) | false

Control for displaying the scatter plot, specified as true or false.

Data Types: logical

PlotOnly — Control for displaying scatter plot without user interface components

false (default) | true

Control for displaying the scatter plot without user interface components, specified as true or false.

Note

If you set PlotOnly to true, you can still display labels for data points by clicking a data point, and you can still adjust the horizontal fold change lines by click-dragging the lines.

Data Types: logical

Output Arguments

Intensity — Intensity values for microarray gene expression data

DataMatrix object | vector

Intensity values for the microarray gene expression data, returned as a DataMatrix object or a vector. The mairplot function calculates these values as follows:

• When Type is set to "IR", the values are log₁₀ of the product of the DataX and DataY intensities.

• When Type is set to "MA", the values are (1/2)log₂ of the product of the DataX and DataY intensities.

Note

If DataX or DataY is a DataMatrix object, then Intensity is also a DataMatrix object with the same properties.

Ratio — Ratios of microarray gene expression data

DataMatrix object | vector

Ratios of the microarray gene expression data, returned as a DataMatrix object or a vector. The mairplot function calculates these values as log2(DataX./DataY).

Note

If DataX or DataY is a DataMatrix object, then Ratio is also a DataMatrix object with the same properties.

References

[1] Quackenbush, J. Microarray Data Normalization and Transformation. Nature Genetics suppl. 32 (2002): 496–501.

[2] Dudoit, S., Y.H. Yang, M.J. Callow, and T.P. Speed. Statistical Methods for Identifying Differentially Expressed Genes in Replicated cDNA Microarray Experiments. Statistica Sinica 12 (2002): 111–139.

Version History

Introduced before R2006a