plotRGB - negative values

Amom--

If your PCA axis scores are centered (mean=0) as is customary, simply

standardize each one to range -0.5:0.5 or -128:127 (with floor to convert

to integers), and then add 0.5 or 128 to center at 0.5 or 127.

Assuming that you're trying to false-color plot the first 3 PCA axes, the

decision you need to make is whether you want to standardize each axis

independently, so that each ranges from 0:255, or whether you want to

standardize the axis with the greatest range to 0:255, then use that

scaling on the other 2 axes to reflect their reduced variation.  Either way

is 'correct', they emphasize different variation in your data.

Depending on the format of your PCA data, you may need to *apply the range

function.  If PCA is an X by 3 matrix with PCA axes as columns, something

like:

Ranges <- apply(PCA,FUN=range,MARGIN=2)

scaledPCA <- scale(PCA,center=rep(-.5,3),scale=Ranges)

should work.

If you want all axes scaled by the longest axis, then something like:

maxRange <- max(apply(PCA,FUN=range,MARGIN=2))

scaledPCA <- scale(PCA,center=rep(-0.5,3),scale=rep(maxRange,3))

might work.  [Note that you could modify this if you needed to scale by

eigenvalues.]

If your PCA values are already in a RasterStackBrick object named

PCAbrick, scale has a method for Raster* objects, but you need to use

cellStats rather than apply and range:

Ranges <- cellStats(PCAbrick,stat='range')

scaledPCAbrick <- scale(PCAbrick,center=c(-0.5,3),scale=Ranges)

[If your raster is "very large", you might have to call cellStats

separately for max and min instead of once for range: see ?cellStats.]

I hope that this is sufficient guidance, and that you can fix any errors

in my untested code.

Tom

On Fri, Aug 9, 2013 at 9:02 AM, amluiz <[hidden email]> wrote:

Thanks Etienne

I was trying to plot three PCA axes (each one representing R, G and B

color bands) in the map, but without success in R. I only can do this in

GIS software...

Any suggestion?

Date: Tue, 6 Aug 2013 13:51:55 -0700

From: [hidden email]

To: [hidden email]

Subject: Re: plotRGB - negative values

        Amom, you could probably offset your values and make sure you set

scale to

the right value. If your lowest value is 1 and the highest value then

becomes 2, then something like

plotRGB(all.pca + 1, scale = 2)

I don't think you can use negative values in plotRGB.

Etienne

2013/8/6 amluiz <[hidden email]>

Hello,

I'm trying to use plotRGB. But I've negative values in my rasters cells

and

I get the following error:

plotRGB(all.pca)

Error in rgb(RGB[, 1], RGB[, 2], RGB[, 3], alpha = alpha, max = scale) :

  color intensity -1, not in 0:255

Is there some way to solve this?

Thanks in advance,

Amom

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