[R-sig-Geo] plotRGB - negative values

Fri Aug 9 21:48:07 CEST 2013

Thanks Philippi, it worked well...
Best,
Amom

Date: Fri, 9 Aug 2013 10:07:28 -0700
From: ml-node+s2731867n7584381h27 at n2.nabble.com
To: amommendes at hotmail.com
Subject: Re: plotRGB - negative values

	Oops, one slight mistake: range() returns a vector of min,max values, so

you need to subtract them:

Ranges <- Ranges[,2] - Ranges[,1]

On Fri, Aug 9, 2013 at 10:02 AM, Tom Philippi <[hidden email]> wrote:

> 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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>>

>> >

>>

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