magicaxis (version 2.4.5)

magmap: Value remapper

Description

This function allows the use to remap a vector of values onto a different system. For instance you might have values stretching from -10 to 100 which you want mapped from 0 to 2/3 so you can then sue the output as an input for point colour or size. It allows clipping of values, rejection of bad values, and log stretching.

Usage

magmap(data, locut = 0, hicut = 1, flip = FALSE, range = c(0, 2/3), type = "quan",
stretch = 'lin', stretchscale = 1, bad = NA, clip = '')

Value

map

The remapped data. This is the same length and order as the input data.

datalim

The a vector of the low and high limits actually applied to the data. Unless type='num' this will probably be different to the lo and hi arguments provided.

maplim

The output range (same is the requested input range, but included for book-keeping).

loclip

The fraction of objects clipped from the input data at the low end.

hiclip

The fraction of objects clipped from the input data at the high end.

Arguments

data

A vector of values. This can contain bad values (NA, NaN, infinite), but these will be ignored during mapping and set to the value of input parameter 'bad'.

locut

The low limit to clip the data at (what this means varies depending on the 'type' option). This should be a single value.

hicut

The high limit to clip the data at (what this means varies depending on the 'type' option). This should be a single value.

flip

Should the scaling be flipped. This allows numbers from 0 to 10 to be mapped from 1 to 0 (so ordered back to front with respect to the input).

range

The numerical range of the output mapping which should be a vector of length two specifying c(low,high).

type

The type of mapping attempted. Options are 'quan' (default), 'num', 'sig' and 'rank'.

stretch

stretch='lin' gives linear mapping. stretch='log' gives logarithmic mapping. stretch='atan' gives atan mapping. stretch='asinh' gives asinh mapping. stretch='sqrt' gives sqrt mapping. stretch='cdf' gives CDF mapping onto the cumulative range 0-1

stretchscale

A number to multiply the data by before applying the stretch. This only has a user impact for stretch='atan' and stretch='asinh' since it controls what parts of the data is in the linear or logarithmic regime of the stretch procedure. If set to 'auto' it uses 1/median(abs(data)) to find a useful scale.

bad

Sets the value that NA, NaN and infinite input data should be set to in the final map output. This should be thought of in the context of the range argument, i.e. if bad=range[1] then bad values will be the low range value and if bad=range[2] bad values will be the high range value.

clip

By default clipped values inherit the nearest lo/hi value (depending on which side they are clipped). Setting clip='NA' will set values outside the 'lo' and 'hi' values to be NA (currently this is the only other clip option).

Author

Aaron Robotham

Details

type='quan' means the lo and hi options are interpreted as the quantile limits to clip the data at (so lo=0.05 and hi 0.95 would clip the data at the 5% and 95% quantile limits and scale values between these). type='num' interprets lo and hi as the exact values to clip the data at and scale between. type='sig' treats lo and hi as the sigma offsets in a Normal distribution, with the probabilities at these positions used to clip and scale that data (so lo=-1 and hi=1 is interpretted as +/- 1 sigma, so the data is clipped and scaled at the 16% and 84% levels, i.e. the 1 sigma range). type='rank' means the data mapping is done by rank value only, with lo and hi specifying the quantile limits used to clip and scale the ranks. In all cases lo and hi clipped values are set to the relevant extreme values of 'range'.

If range is between 1 and 100 and stretch='lin' the midpoint in the mapping will be 50.5. If stretch='log' the midpoint becomes 10. This enhances the local dynamic range of the mapping for data that has a logarithmic distribution.

See Also

magimage, magbar

Examples

set.seed(650)
temp=cbind(runif(100),runif(100))
temp=cbind(temp,sqrt(temp[,1]^2+temp[,2]^2))
magplot(temp)
magplot(temp[,1:2],col=hsv(h=magmap(temp[,3])$map))

# A different mapping type:
magplot(temp[,1:2],col=hsv(h=magmap(temp[,3],type='rank')$map))

# Flipped:
magplot(temp[,1:2],col=hsv(h=magmap(temp[,3],flip=TRUE,type='rank')$map))

# Example of linear/log/atan/asinh mapping:
temp=cbind(temp,10^temp[,3])
magplot(temp[,1:2],col=hsv(h=magmap(temp[,4])$map))
magplot(temp[,1:2],col=hsv(h=magmap(temp[,4],stretch='log')$map))
magplot(temp[,1:2],col=hsv(h=magmap(temp[,4],stretch='atan')$map))
magplot(temp[,1:2],col=hsv(h=magmap(temp[,4],stretch='asinh')$map))

#atan and asinh can be useful when data spans negative to positive:
temp=cbind(temp,temp[,4]-10)
magplot(temp[,1:2],col=hsv(h=magmap(temp[,5],stretch='atan')$map))
magplot(temp[,1:2],col=hsv(h=magmap(temp[,5],stretch='asinh')$map))
#effect of stretchscale
magplot(temp[,1:2],col=hsv(h=magmap(temp[,5],stretch='atan',stretchscale=0.5)$map))
magplot(temp[,1:2],col=hsv(h=magmap(temp[,5],stretch='atan',stretchscale=2)$map))
magplot(temp[,1:2],col=hsv(h=magmap(temp[,5],stretch='asinh',stretchscale=0.5)$map))
magplot(temp[,1:2],col=hsv(h=magmap(temp[,5],stretch='asinh',stretchscale=2)$map))

#Using multiple mappings for plots:
magplot(temp[,1:2],col=hsv(h=magmap(temp[,4],stretch='log')$map),
cex=magmap(temp[,3],lo=0.5,hi=1,range=c(1,6),type='num')$map)

#Different combinations of mapping options:
magmap(c(-1,0.1,1,NA,0.3,3),lo=0,hi=2.5,type='num',stretch='lin',bad=0.5)$map
magmap(c(-1,0.1,1,NA,0.3,3),lo=0.1,hi=0.9,type='quan',stretch='log',bad=0.8)$map
magmap(c(-1,0.1,1,NA,0.3,3),lo=-1,hi=1,type='sig',stretch='asinh',bad=0,stretchscale=2)$map
magmap(c(-1,0.1,1,NA,0.3,3),type='rank',stretch='atan',bad=NA,stretchscale=2)$map

#Example showing using asinh to generate a different axis mapping:
datastretch=cbind(runif(1e3),10^runif(1e3,0,4)-10^runif(1e3,0,4))
#This isn't a very helpful view of the data
magplot(datastretch[,1:2])
#This only shows the positive half of the data:
magplot(datastretch[,1:2],log='y')
#We can do a better job by remapping using the asinh option in magmap:
datastretch=cbind(datastretch,magmap(datastretch[,2],lo=-1e4,hi=1e4,range=c(0,1),
type='num',stretch='asinh')$map)
asinhticks=magmap(c(-10^(4:0),0,10^(0:4)),lo=-1e4,hi=1e4,range=c(0,1),type='num',
stretch='asinh')$map
magplot(datastretch[,1],datastretch[,3],side=1)
axis(2,asinhticks,labels=c(-10^(4:0),0,10^(0:4)))
abline(h=magmap(0,lo=-1e4,hi=1e4,range=c(0,1),type='num',stretch='asinh')$map)