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maboxplot

Create box plot for microarray data

Syntax

maboxplot(MAData)
maboxplot(MAData, ColumnName)
maboxplot(MAStruct, FieldName)
H = maboxplot(...)
[H, HLines] = maboxplot(...)
maboxplot(..., 'Title', TitleValue, ...)
maboxplot(..., 'Notch', NotchValue, ...)
maboxplot(..., 'Symbol', SymbolValue, ...)
maboxplot(..., 'Orientation', OrientationValue, ...)
maboxplot(..., 'WhiskerLength', WhiskerLengthValue, ...)
maboxplot(..., 'BoxPlot', BoxPlotValue, ...)

Arguments

MAData DataMatrix object, numeric array, or a structure containing a field called Data. The values in the columns of MAData will be used to create box plots. If a DataMatrix object, the column names are used as labels in the box plot.
ColumnName An array of column names corresponding to the data in MAData used as labels in the box plot.
MAStructA microarray data structure.
FieldNameA field within the microarray data structure, MAStruct. The values in the field FieldName will be used to create box plots.
TitleValueCharacter vector to use as the title for the plot. The default title is FieldName.
NotchValue

Logical specifying the type of boxes drawn. Choices are:

  • true — Notched boxes

  • false — Square boxes

Default is false.
OrientationValue

Character vector specifying the orientation of the box plot. Choices are:

  • 'Vertical'

  • 'Horizontal' (default)

WhiskerLengthValueValue specifying the maximum length of the whiskers as a function of the interquartile range (IQR). The whisker extends to the most extreme data value within WhiskerLengthValue*IQR of the box. Default = 1.5. If WhiskerLengthValue equals 0, then maboxplot displays all data values outside the box, using the plotting symbol Symbol.
BoxPlotValue

A cell array of property name/property value pairs to pass to the Statistics and Machine Learning Toolbox™ boxplot function, which creates the box plot. For valid pairs, see the boxplot function.

Description

maboxplot(MAData) displays a box plot of the values in the columns of MAData. MAData can be a DataMatrix object, numeric array, or a structure containing a field called Data, containing microarray data.

maboxplot(MAData, ColumnName) labels the box plot column names.

maboxplot(MAStruct, FieldName) displays a box plot of the values in the field FieldName in the microarray data structure MAStruct. If MAStruct is block based, maboxplot creates a box plot of the values in the field FieldName for each block.

Note

If you provide MAStruct, without providing FieldName, maboxplot uses the Signal element in the ColumnNames field of MAStruct, if Affymetrix®data, or the first element in the ColumnNames field of MAStruct, otherwise.

H = maboxplot(...) returns the handle of the box plot axes.

[H, HLines] = maboxplot(...) returns the handles of the lines used to separate the different blocks in the image.

maboxplot(..., 'PropertyName', PropertyValue, ...) calls maboxplot with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

maboxplot(..., 'Title', TitleValue, ...) allows you to specify the title of the plot. The default TitleValue is FieldName.

maboxplot(..., 'Notch', NotchValue, ...) if NotchValue is true, draws notched boxes. The default is false to show square boxes.

maboxplot(..., 'Symbol', SymbolValue, ...) allows you to specify the symbol used for outlier values. The default Symbol is '+'.

maboxplot(..., 'Orientation', OrientationValue, ...) allows you to specify the orientation of the box plot. The choices are 'Vertical' and 'Horizontal'. The default is 'Vertical'.

maboxplot(..., 'WhiskerLength', WhiskerLengthValue, ...) allows you to specify the whisker length for the box plot. WhiskerLengthValue defines the maximum length of the whiskers as a function of the interquartile range (IQR) (default = 1.5). The whisker extends to the most extreme data value within WhiskerLength*IQR of the box. If WhiskerLengthValue equals 0, then maboxplot displays all data values outside the box, using the plotting symbol Symbol.

maboxplot(..., 'BoxPlot', BoxPlotValue, ...) allows you to specify arguments to pass to the boxplot function, which creates the box plot. BoxPlotValue is a cell array of property name/property value pairs. For valid pairs, see the boxplot function.

Examples

collapse all

This example shows how to display box plots for microarray data.

Load the MAT-file, provided with the Bioinformatics Toolbox™ software, that contains yeast data. This MAT-file includes three variables: yeastvalues , a matrix of gene expression data, genes , a cell array of GenBank® accession numbers for labeling the rows in yeastvalues, and times , a vector of time values for labeling the columns in yeastvalues.

load yeastdata

Show the box plot of gene expression data.

maboxplot(yeastvalues,times);
xlabel('Sample Times');

Use the gprread function to create a structure containing microarray data, and plot the data using name-value pair arguments of the maboxplot function.

madata = gprread('mouse_a1wt.gpr');
maboxplot(madata,'F635 Median - B635','TITLE', 'Cy5 Channel FG - BG');

Introduced before R2006a

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