Simatrix object (Multivariate Analysis Toolbox for Matlab®)

This object represents a data matrix that describes pairwise similarities between the samples. It inherits from the parent object ssmatrix.

Navigate to:     General Description     Class Structure     Class Construction     Class Functions

Each field can be accessed by the dot (.) operation, or by the GET function. The GET function can work on multiple instances simultaneously. Most fields, except for those that are Dependent, can be modified using the dot (.) operation, or by the SET function.

		Field	Description	Type	Default	Dedicated Get/Set Function
		ss_type	type of sample-sample data, fixed on 'similarity'	string	'similarity'
		sim_type	type of similarity	string	''
		type	Inherited from ssmatrix. Type of matrix. It is always 'sample-sample'	string	'sample-sample'
		is_square	Inherited from ssmatrix. true if the row-samples are identical to the column-samples.	logical	false
		name	Inherited from datamatrix. name of object, should be short and used as identifier. This field will never be empty.	string	'unnamed'
		description	Inherited from datamatrix. verbal description of the class content.	string	''
		source	Inherited from datamatrix. verbal description of the source of information.	string	''
		row_name	Inherited from datamatrix. Name of the row-category (for example, in gene arrays it can be "tissue").	string	''
		row_sampleset	Inherited from datamatrix. A sampleset describing the row-samples.	sampleset	[]
		row_groupings	Inherited from datamatrix. grouping objects associated with the row-samples.	grouping array	[]
		col_name	Inherited from datamatrix. Name of the column-category (for example, in gene arrays it can be "genes").	string	''
		col_sampleset	Inherited from datamatrix. A sampleset describing the column-samples.	sampleset	[]
		col_groupings	Inherited from datamatrix. grouping objects associated with the column-samples.	grouping array	[]
		matrix	Inherited from datamatrix. the data matrix.	double	[]
		transformations	Inherited from datamatrix. keeping track on transformations that had been applied previously on the matrix.	structure	[]
	Dependent	no_rows	Inherited from datamatrix. number of row-samples.	integer scalar	0	norows
	Dependent	no_cols	Inherited from datamatrix. number of column-samples.	integer scalar	0	nocols

Empty instance (scalar)

an empty simatrix instance, with all fields initialized to their default values.

syntax: sim = simatrix;

Empty instance (matrix)

an array of empty simatrix instances.

syntax: sim = simatrix(size,'size');

Copy constructor

one simatrix instance is copied into another.

syntax: sim_destination = simatrix(sim_origin);

Construction by field names

an instance is formed by directly providing field values. Any field which is not dependent is permitted.

syntax: sim = simatrix(field_name, field_value, ...);

Reading-in a matrix

an instance is formed by reading-in an externally provided matrix.

syntax: sim = simatrix(matrix);

Casting an ssmatrix

Casting from a ssmatrix instance.

syntax: sim = simatrix(ssm);

Computations:

ssm2lap

transforms ssmatrix to Laplacian (and Degree). Source: ssmatrix.

Display:

show

displays class content. Source: ssmatrix.

Information extraction:

colid

finds the IDs of a list of column-variables. Source: datamatrix.

rowid

finds the IDs of a list of row-variables. Source: datamatrix.

SET/GET functions:

colnames

retrieves the column-variable names. Source: datamatrix.

get

get method

nocols

retrieves the number of columns in DATAMATRIX instances. Source: datamatrix.

norows

retrieves the number of rows in DATAMATRIX instances. Source: datamatrix.

rownames

retrieves the row-variable names. Source: datamatrix.

set

set method

Transformations:

deletecols

eliminate columns from a DATAMATRIX instance. Source: datamatrix.

deleterows

eliminate rows from a DATAMATRIX instance. Source: datamatrix.

modify

modifies sample-sample relationships. Source: ssmatrix.

Visualization:

eigenproj

computes the eigenprojection of a similarity matrix.

plot

plots a distance matrix Source: ssmatrix.