BoxPlotDistance: Box plots of one distance matrix categorized against another...

In IntClust: Integrated Data Analysis via Clustering

Description

Given two distance matrices, the function categorizes one distance matrix and produces a box plot from the other distance matrix against the created categories. The option is available to choose one of the plots or to have both plots. The function also works on outputs from ADEC and CEC functions which do not have distance matrices but incidence matrices.

Usage

BoxPlotDistance(Data1, Data2, type=c('data','dist','clusters'), distmeasure="tanimoto",
normalize=FALSE,method=NULL,lab1, lab2, limits1=NULL, limits2=NULL, plot = 1,
StopRange=FALSE,plottype="new",location=NULL)

Arguments

Data1	The first data matrix, cluster outcome or distance matrix to be plotted.
Data2	The second data matrix, cluster outcome or distance matrix to be plotted.
type	Type indicates the kind of data provided as input. Should be one of "data", "cluster" or "distance". The type "cluster" is used if the data is the output of one of the integrated data cluster functions of the package.
distmeasure	Choice of metric for the dissimilarity matrix (character) and should only be specified if type is "data". Should be one of "tanimoto", "euclidean", "jaccard","hamming".
normalize	Logical. Indicates whether to normalize the distance matrices or not. This is recommended if different distance types are used. More details on normalization in Normalization.
method	A method of normalization. Should be one of "Quantile","Fisher-Yates", "standardize","Range" or any of the first letters of these names.
lab1	The label to plot for Data1.
lab2	The label to plot for Data2.
limits1	The limits for the categories of Data1.
limits2	The limits for the categories of Data2.
plot	The type of plots: 1 - Plot the values of Data1 versus the categories of Data2. 2 - Plot the values of Data2 versus the categories of Data1. 3 - Plot both types 1 and 2.
StopRange	Logical. Indicates whether the distance matrices with values not between zero and one should be standardized to have so. If FALSE the range normalization is performed. See Normalization. If TRUE, the distance matrices are not changed. This is recommended if different types of data are used such that these are comparable.
plottype	Should be one of "pdf","new" or "sweave". If "pdf", a location should be provided in "location" and the figure is saved there. If "new" a new graphic device is opened and if "sweave", the figure is made compatible to appear in a sweave or knitr document, i.e. no new device is opened and the plot appears in the current device or document.
location	If plottype is "pdf", a location should be provided in "location" and the figure is saved there.

Value

One/multiple box plots.

Author(s)

Marijke Van Moerbeke

Examples

data(fingerprintMat)
data(targetMat)

MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)


BoxPlotDistance(MCF7_F,MCF7_T,type="cluster",lab1="F",lab2="T",limits1=c(0.3,0.7),
limits2=c(0.3,0.7),plot=1,StopRange=FALSE,plottype="new", location=NULL)

Example output

Warning messages:
1: Duplicated aesthetics after name standardisation: size 
2: Duplicated aesthetics after name standardisation: size 

IntClust documentation built on May 2, 2019, 5:23 p.m.