getDensity Class Reference

Inheritance diagram for getDensity:

Public Types
enum	Events { checkData }

Public Member Functions
function	getDensity (in varargin)
	Class constructor.
function	run (in obj)
	Our main RUN method.
function	scatterColumns (in obj, in c1, in c2)
function	jitterData (in obj, in datain, in jitter)
function get	nColumns (in obj)
function get	isDataEqualLength (in obj)
function get	plotX (in obj)
function get	plotY (in obj)
function get	uniquecases (in obj)
function set	x (in obj, in value)
function set	y (in obj, in value)
function set	columnlabels (in obj, in value)
function set	cases (in obj, in value)
function	haveData (in obj)
function	reset (in obj)
	reset the data to empty
function	doSinglePlots (in obj, in pn)

Static Public Member Functions
static function	violin (in x, in y, in varargin)

Public Attributes
Property	comments
	comments to add to this data comparison
Property	x
	our first data group, plotted along the abscissa
Property	y
	our second data group, plotted along the ordinate
Property	xrownames
	a cell of names for each row
Property	yrownames
	a cell of names for each row
Property	nboot
	number of bootstrap iterations default: 1000
Property	avgFunction
	function handle to bootstrap default: @mean
Property	alpha
	P value to use for all statistics.
Property	legendtxt
	A cell list of the main X and Y data, i.e. {'Control','Drug'}.
Property	columnlabels
	if X/Y have more than 1 column, you can detail column names here
Property	dogauss
	Add gaussian fits to the histograms? default: true.
Property	addjitter
	add jitter to scatterplot? 'x', 'y', 'both', 'equal', 'none'
Property	cases
	celllist of case names the same length as X/Y
Property	nominalcases
	are our cases nominal or ordinal?
Property	dooutlier
	remove outliers using 'grubb', 'rosner', 'limit', '3SD' or 'none'
Property	rosnern
	rosner outlier number of outliers
Property	outlierp
	p to use for outlier removal for rosner and grubb
Property	outlierlimit
	outlier limit for limit method
Property	jitterfactor
	scalefactor for jitter of scatter plot
Property	singleplots
	do we spit out each plot in its own figure for easy export?
Property	showoriginalscatter
	do we show the original points in the scatter before scattering them?
Property	autorun
	if we are passed data on construction, run straight away
Property	bartype
	how to plot the histogram
Property	barwidth
	width of histogram bars
Property	verbose
	are we verbose printing to command line?
Property	scaleaxes
	do we scale the axes to be equal for the scatterplots
Property	showunityline
	do we show the unity line for the scatterplot?
Property	nBins
	number of bins for histogram
Property	centreBins
	centre histogram bins
Property	densityKernel
	density kernel to use, 'normal', 'box', 'triangle', 'epanechnikov'
Property	densityFunction
	density function, 'pdf', 'cdf','icdf', 'survivor', 'cumhazard'
Property	densityBounds
	density bounds; 'unbounded', 'positive' or 2-element vector for lower and upper
Property	index
	for multiple columns only run a subset; empty runs all.
Property	normaliseScatter
	normalise (Z-score) values to plot on scatter?
Property	doDistribution
	show distribution plot underneath box plot?
Property	doMedianCI
	do a median CI, takes longer if dataset is large...

Member Enumeration Documentation

Events

enum getDensity::Events

Enumerator
checkData

                                 :nVals;
            end

Constructor & Destructor Documentation

getDensity()

function getDensity::getDensity

(

in

varargin

)

Class constructor.

More detailed description of what the constructor does.

Parameters

args	are passed as a structure of properties which is parsed.

Returns

instance of class.

Member Function Documentation

cases()

function set getDensity::cases	(	in	obj,
		in	value
	)

Parameters

obj	this instance object

columnlabels()

function set getDensity::columnlabels	(	in	obj,
		in	value
	)

Parameters

obj	this instance object

doSinglePlots()

function getDensity::doSinglePlots	(	in	obj,
		in	pn
	)

Parameters

obj	this instance object

haveData()

function getDensity::haveData

(

in

obj

)

Parameters

obj	this instance object

isDataEqualLength()

function get getDensity::isDataEqualLength

(

in

obj

)

Parameters

obj	this instance object

jitterData()

function getDensity::jitterData	(	in	obj,
		in	datain,
		in	jitter
	)

Parameters

obj	this instance object

nColumns()

function get getDensity::nColumns

(

in

obj

)

Parameters

obj	this instance object

plotX()

function get getDensity::plotX

(

in

obj

)

Parameters

obj	this instance object

plotY()

function get getDensity::plotY

(

in

obj

)

Parameters

obj	this instance object

reset()

function getDensity::reset

(

in

obj

)

reset the data to empty

Parameters

obj	this instance object

run()

function getDensity::run

(

in

obj

)

Our main RUN method.

This performs the analysis and plots the results for the stored data.

Parameters

obj	the class object automatically passed in

Returns

outs a structure with the analysis results if needed.

scatterColumns()

function getDensity::scatterColumns	(	in	obj,
		in	c1,
		in	c2
	)

Parameters

obj	this instance object

uniquecases()

function get getDensity::uniquecases

(

in

obj

)

Parameters

obj	this instance object

violin()

static function getDensity::violin ( in  x, in  y, in  varargin  )

static

x()

function set getDensity::x	(	in	obj,
		in	value
	)

Parameters

obj	this instance object

y()

function set getDensity::y	(	in	obj,
		in	value
	)

Parameters

obj	this instance object

Member Data Documentation

addjitter

Property getDensity::addjitter

add jitter to scatterplot? 'x', 'y', 'both', 'equal', 'none'

alpha

Property getDensity::alpha

P value to use for all statistics.

autorun

Property getDensity::autorun

if we are passed data on construction, run straight away

avgFunction

Property getDensity::avgFunction

function handle to bootstrap default: @mean

bartype

Property getDensity::bartype

how to plot the histogram

barwidth

Property getDensity::barwidth

width of histogram bars

cases

Property getDensity::cases

celllist of case names the same length as X/Y

centreBins

Property getDensity::centreBins

centre histogram bins

columnlabels

Property getDensity::columnlabels

if X/Y have more than 1 column, you can detail column names here

comments

Property getDensity::comments

comments to add to this data comparison

densityBounds

Property getDensity::densityBounds

density bounds; 'unbounded', 'positive' or 2-element vector for lower and upper

densityFunction

Property getDensity::densityFunction

density function, 'pdf', 'cdf','icdf', 'survivor', 'cumhazard'

densityKernel

Property getDensity::densityKernel

density kernel to use, 'normal', 'box', 'triangle', 'epanechnikov'

doDistribution

Property getDensity::doDistribution

show distribution plot underneath box plot?

dogauss

Property getDensity::dogauss

Add gaussian fits to the histograms? default: true.

doMedianCI

Property getDensity::doMedianCI

do a median CI, takes longer if dataset is large...

dooutlier

Property getDensity::dooutlier

remove outliers using 'grubb', 'rosner', 'limit', '3SD' or 'none'

index

Property getDensity::index

for multiple columns only run a subset; empty runs all.

jitterfactor

Property getDensity::jitterfactor

scalefactor for jitter of scatter plot

legendtxt

Property getDensity::legendtxt

A cell list of the main X and Y data, i.e. {'Control','Drug'}.

nBins

Property getDensity::nBins

number of bins for histogram

nboot

Property getDensity::nboot

number of bootstrap iterations default: 1000

nominalcases

Property getDensity::nominalcases

are our cases nominal or ordinal?

normaliseScatter

Property getDensity::normaliseScatter

normalise (Z-score) values to plot on scatter?

outlierlimit

Property getDensity::outlierlimit

outlier limit for limit method

outlierp

Property getDensity::outlierp

p to use for outlier removal for rosner and grubb

rosnern

Property getDensity::rosnern

rosner outlier number of outliers

scaleaxes

Property getDensity::scaleaxes

do we scale the axes to be equal for the scatterplots

showoriginalscatter

Property getDensity::showoriginalscatter

do we show the original points in the scatter before scattering them?

showunityline

Property getDensity::showunityline

do we show the unity line for the scatterplot?

singleplots

Property getDensity::singleplots

do we spit out each plot in its own figure for easy export?

verbose

Property getDensity::verbose

are we verbose printing to command line?

x

Property getDensity::x

our first data group, plotted along the abscissa

xrownames

Property getDensity::xrownames

a cell of names for each row

y

Property getDensity::y

our second data group, plotted along the ordinate

yrownames

Property getDensity::yrownames

a cell of names for each row

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The documentation for this class was generated from the following file:

• data/getDensity.m