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Last data update: 2014.03.03

R: Image Scatter Plot Matrix for Large Datasets

ipairs

R Documentation

Image Scatter Plot Matrix for Large Datasets

Description

Produces an image scatter plot matrix of large datasets where the colors encode the density of the points in the scatter plots.

Usage

ipairs(x,
       pixs = 1, zmax = NULL, ztransf=function(x){x},
       colramp = IDPcolorRamp, cex = par("cex"),
       lab.diag, cex.diag = NULL,
       main = NULL, d.main = 1.5, cex.main = 1.5*par("cex.main"),
       legend = TRUE, d.legend = 1.5, cex.axis = 0.8*par("cex.axis"),
       nlab.axis = 5, minL.axis = 2, las = 1, border = FALSE,
       mar = rep(0,4), oma = c(3,3,1,0), mgp = c(2,0.5,0)*cex.axis,
       tcl = -0.3, ...)

Arguments

`x`	data.frame or matrix
`pixs`	Pixel size in mm on the plotting device.
`zmax`	Maximum number of counts per pixel in the plot. When NULL, each scatter plot has its individual scale. If a number >= maximum number of counts per pixel is supplied, the scale will be identical for all scatter plots. The maximum number of counts per pixel is delivered by the return value.
`ztransf`	Function to transform the counts per pixel, which will be mapped by the function in `colramp` to well defined colors. The user has to make sure that the transformed counts lie in the range [0,zmax], where zmax is any positive number (>=2).
`colramp`	Color ramp to encode the number of counts within a pixel.
`cex`	See Argument `cex` in `par`
`lab.diag`	Labels of columns, written into the diagonal of the matrix. When `NULL`, the names of x are used.
`cex.diag`	Magnification used for text in diagonal relative to the current setting of cex. When `NULL`, they are calculated automatically.
`main`	Titel. When `NULL`
`d.main`	Vertical distance between upper border of scatter plots and the title line in multiples of title height.
`cex.main`	Magnification used for title relative to the current setting of cex.
`legend`	Logical. When `FALSE`, no legend is plotted and space is saved in figure region.
`d.legend`	Horizontal distance between right border of scatter plots and legend in multiples of title height.
`cex.axis`	Magnification used for axis annotation relative to the current setting of cex.
`nlab.axis`	Approximate number of labels on axes.
`minL.axis`	The minimum length of the abbreviations of factor levels, used to label the axes ticks.
`las`	Orientation of labels on axes.
`border`	Logical. When `TRUE`, a border is drawn around the individual colors in the legend.
`mar, oma`	Margin and outer margin respectively. Cf. `par`
`mgp, tcl`	Cf. `par`
`...`	Additional arguments to `par`

Details

The idea is similar to gplot.hexbin. The hexagons are better suited to reflect the density of points in a plane than the squares used here. Nevertheless squares are, contrary to hexagons, invariant to reflexions at the x- and y-axis and therefore better suited for scatter plot matrices and also for plotting factors.

The code is based on R function pairs V1.7.

Value

Maximum number of counts per Pixel found. Additional elements are returned when verbose == TRUE.

Note

When you get the error message "Zmax too small! Densiest aereas are out of range!" you must run the function with identical parameters but without specifying zmax. The value returned gives you the minimum value allowed for zmax.

Author(s)

Andreas Ruckstuhl, Rene Locher

Examples

## Small numbers of different values are plotted nicer
## when converted to factors
AQ <- airquality
AQ$Month <- as.factor(AQ$Month)

zmax <- ipairs(AQ, pixs=2, main="Air Quality")
ipairs(AQ, pixs=2, zmax=zmax, main="Air Quality",border=TRUE)

## example with factors
ipairs(iris,pixs=2)

## a really huge dataset
if(require(SwissAir)) {
  data(AirQual)

  ## low correlation
  ipairs(AirQual[,c("ad.O3","lu.O3","sz.O3")],
         ztransf=function(x){x[x<1] <- 1; log2(x)})

  ipairs(AirQual[,c("ad.NO","lu.NO","sz.NO")],
         ztransf=function(x){x[x<1] <- 1; log2(x)})

  ## high correlation
  Ox <- AirQual[,c("ad.O3","lu.O3","sz.O3")]+
    AirQual[,c("ad.NOx","lu.NOx","sz.NOx")]-
      AirQual[,c("ad.NO","lu.NO","sz.NO")]
  names(Ox) <- c("ad","lu","sz")
  ipairs(Ox, ztransf=function(x){x[x<1] <- 1; log2(x)})

  ## cf. ?AirQual for the explanation of the physical and
  ## chemical background
} else print("Package SwissAir is not available")

Results


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(IDPmisc)
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IDPmisc/ipairs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ipairs
> ### Title: Image Scatter Plot Matrix for Large Datasets
> ### Aliases: ipairs
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## Small numbers of different values are plotted nicer
> ## when converted to factors
> AQ <- airquality
> AQ$Month <- as.factor(AQ$Month)
> 
> zmax <- ipairs(AQ, pixs=2, main="Air Quality")
> ipairs(AQ, pixs=2, zmax=zmax, main="Air Quality",border=TRUE)
> 
> ## example with factors
> ipairs(iris,pixs=2)
> 
> ## a really huge dataset
> if(require(SwissAir)) {
+   data(AirQual)
+ 
+   ## low correlation
+   ipairs(AirQual[,c("ad.O3","lu.O3","sz.O3")],
+          ztransf=function(x){x[x<1] <- 1; log2(x)})
+ 
+   ipairs(AirQual[,c("ad.NO","lu.NO","sz.NO")],
+          ztransf=function(x){x[x<1] <- 1; log2(x)})
+ 
+   ## high correlation
+   Ox <- AirQual[,c("ad.O3","lu.O3","sz.O3")]+
+     AirQual[,c("ad.NOx","lu.NOx","sz.NOx")]-
+       AirQual[,c("ad.NO","lu.NO","sz.NO")]
+   names(Ox) <- c("ad","lu","sz")
+   ipairs(Ox, ztransf=function(x){x[x<1] <- 1; log2(x)})
+ 
+   ## cf. ?AirQual for the explanation of the physical and
+   ## chemical background
+ } else print("Package SwissAir is not available")
Loading required package: SwissAir
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>