Bioinformatics Toolbox™

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

Description

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

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

% Using a structure
geoStruct = getgeodata('GSM1768');
maboxplot(geoStruct, 'title', 'GSM1768');

% For block-based data
madata = gprread('mouse_a1wt.gpr');
maboxplot(madata,'F635 Median','Boxplot',...
          {'Factorlabelorientation', 'horizontal'});
figure
maboxplot(madata,'F635 Median - B635','TITLE',...
          'Cy5 Channel FG - BG');

See Also

Bioinformatics Toolbox™ functions: magetfield, maimage, mairplot, maloglog, malowess, manorm, mavolcanoplot

Statistics Toolbox function: boxplot

knnimpute

mafdr