similarity matrix; if missing it will be calculated from data by similarity.variables
x
name of the predictor variable (as used in data and S) of main interest, for which confounders / collinearities shall be detected
y
name of the outcome variable (as used in data and S)
labels
variable names used for plotting; have to be in corresponding order with columns of data; if missing, names of data are used
returnS
shall similarity matrix be returned?
plotLegend
shall (default) legend be shown, indicating categorical and continuous variables
col
symbol and label color; by default categorical variables are shown in purple, continuous variables in black
pch
plotting symbol, default 16
font
font of plotted labels; by default names of variables x and y are shown in bold
xlim, ylim
axis limits
...
graphical parameters passed to plot
Details
The similarities of all variables in a dataset with two variables of special interest (i.e. predictor and outcome of a regression model) are simultaneously visualized in a scatter plot, where the x-axis shows similarities to the predictor and the y-axis similarities to the outcome. The height of the predictor variable's point indicates its association with the outcome and hence its predicting ability. Variables in the upper right part are potential confounders for which prediction model should be adjusted, or collinear variables that should be removed. Variables in the lower right part are strongly related to the predictor, but not associated with the outcome. Variables very close to the outcome variable's point are potential surrogate outcomes.
Value
Scatterplot of variable similarities. Chosen predictor and outcome variables are highlighted in bold. Categorical/quantitative variables are shown in blue/black by default.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(CluMix)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/CluMix/confounderPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: confounderPlot
> ### Title: Confounder Plot
> ### Aliases: confounderPlot
> ### Keywords: hplot
>
> ### ** Examples
>
> data(mixdata)
>
> confounderPlot(mixdata, x="X2.quant", y="X1.cat")
>
>
>
>
>
> dev.off()
null device
1
>