plot1DProjection {clusterGeneration} | R Documentation |
Plot a pair of clusters and their density estimates, which are projected along a specified 1-D projection direction.
plot1DProjection(y1, y2, projDir, sepValMethod=c("normal", "quantile"), bw="nrd0", xlim=NULL, ylim=NULL, xlab="1-D projected clusters", ylab="density estimates", title="1-D Projected Clusters and their density estimates", font=2, font.lab=2, cex=1.2, cex.lab=1.2, cex.main=1.5, lwd=4, lty1=1, lty2=2, pch1=18, pch2=19, col1=2, col2=4, type="l", alpha=0.05, eps=1.0e-10, quiet=TRUE)
y1 |
Data matrix of cluster 1. Rows correspond to observations. Columns correspond to variables. |
y2 |
Data matrix of cluster 2. Rows correspond to observations. Columns correspond to variables. |
projDir |
1-D projection direction along which two clusters will be projected. |
sepValMethod |
Method to calculate separation index for a pair of clusters projected onto a
1-D space. sepValMethod="quantile" indicates the quantile version of
separation index will be used: sepVal=(L_2-U_1)/(U_2-L_1) where L_i and
U_i, i=1, 2, are the lower and upper alpha/2 sample percentiles
of projected cluster i. sepValMethod="normal" indicates the
normal version of separation index will be used:
sepVal=[(xbar_2-xbar_1)-z_{α/2}(s_1+s_2)]/
[(xbar_2-xbar_1)+z_{α/2}(s_1+s_2)],
where xbar_i and s_i are the sample mean and standard deviation
of projected cluster i.
|
bw |
The smoothing bandwidth to be used by the function density .
|
xlim |
Range of X axis. |
ylim |
Range of Y axis. |
xlab |
X axis label. |
ylab |
Y axis label. |
title |
Title of the plot. |
font |
An integer which specifies which font to use for text (see par ).
|
font.lab |
The font to be used for x and y labels (see par ).
|
cex |
A numerical value giving the amount by which plotting text
and symbols should be scaled relative to the default (see par ).
|
cex.lab |
The magnification to be used for x and y labels relative
to the current setting of 'cex' (see par ).
|
cex.main |
The magnification to be used for main titles relative
to the current setting of 'cex' (see par ).
|
lwd |
The line width, a _positive_ number, defaulting to '1' (see par ).
|
lty1 |
Line type for cluster 1 (see par ).
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lty2 |
Line type for cluster 2 (see par ).
|
pch1 |
Either an integer specifying a symbol or a single character
to be used as the default in plotting points for cluster 1 (see points ).
|
pch2 |
Either an integer specifying a symbol or a single character
to be used as the default in plotting points for cluster 2 (see points ).
|
col1 |
Color to indicates cluster 1. |
col2 |
Color to indicates cluster 2. |
type |
What type of plot should be drawn (see plot ).
|
alpha |
Tuning parameter reflecting the percentage in the two tails of a projected cluster that might be outlying. |
eps |
A small positive number to check if a quantitiy q is equal to zero.
If |q|<eps , then we regard q as equal to zero.
eps is used to check the denominator in the formula of the separation
index is equal to zero. Zero-value denominator indicates two clusters are
totally overlapped. Hence the separation index is set to be -1.
The default value of eps is 1.0e-10.
|
quiet |
A flag to switch on/off the outputs of intermediate results and/or possible warning messages. The default value is TRUE .
|
The ticks along X axis indicates the positions of points of the projected
two clusters. The positions of L_i and U_i, i=1, 2, are also indicated
on X axis, where L_i and U_i are the lower and upper α/2 sample
percentiles of cluster i if sepValMethod="quantile"
.
If sepValMethod="normal"
,
L_i=xbar_i-z_{α/2}s_i, where xbar_i and s_i are the
sample mean and standard deviation of cluster i, and z_{α/2}
is the upper α/2 percentile of standard normal distribution.
sepVal |
value of the separation index for the projected two clusters along
the projection direction projDir .
|
projDir |
projection direction. To make sure the projected cluster 1 is on the
left-hand side of the projected cluster 2, the input projDir
might be changed to -projDir .
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Weiliang Qiu stwxq@channing.harvard.edu
Harry Joe harry@stat.ubc.ca
Qiu, W.-L. and Joe, H. (2006) Separation Index and Partial Membership for Clustering. Computational Statistics and Data Analysis, 50, 585–603.
n1<-50 mu1<-c(0,0) Sigma1<-matrix(c(2,1,1,5),2,2) n2<-100 mu2<-c(10,0) Sigma2<-matrix(c(5,-1,-1,2),2,2) projDir<-c(1, 0) library(MASS) set.seed(1234) y1<-mvrnorm(n1, mu1, Sigma1) y2<-mvrnorm(n2, mu2, Sigma2) y<-rbind(y1, y2) cl<-rep(1:2, c(n1, n2)) b<-getSepProjData(y, cl, iniProjDirMethod="SL", projDirMethod="newton") # projection direction for clusters 1 and 2 projDir<-b$projDirArray[1,2,] plot1DProjection(y1, y2, projDir)