[R] Heatmap fidelity

[Steven Wolf]

Thanks!

-Steve

-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] 
Sent: Thursday, April 26, 2012 9:28 AM
To: Steven Wolf
Cc: r-help at r-project.org
Subject: Re: [R] Heatmap fidelity

On 26/04/2012 9:01 AM, Steven Wolf wrote:
> I'm having a problem when using heatmap.  Even though the diagonal of 
> my matrix is all the same value, the diagonal of my heatmap is not all 
> the same color.  Any suggestions?

heatmap() rescales the matrix by default.  Use

heatmap(abs(psim), scale="none")

to plot the raw data.

Duncan Murdoch

>
>
>
> Here is some reproducible code:
>
> #########################################
>
> # Get data
>
> nba<- read.csv("http://datasets.flowingdata.com/ppg2008.csv", sep=",")
>
>
>
> # Reorder
>
> nba<- nba[order(nba$PTS),]
>
>
>
> # Name the rows and then eliminate the 1st row
>
> row.names(nba)<- nba$Name
>
> nba<- nba[,2:20]
>
> # nba2<- nba[1:10,] ## use these if you only want to look @ 10 players
>
>
>
> # Compute how "similar" players are by doing a correlation between 
> their statistical sets
>
> psim = cor(t(nba))
>
> # psim2 = cor(t(nba2))
>
>
>
> # Note: everyone has a self-correlation of 1
>
> diag(abs(psim))
>
> # diag(abs(psim2))
>
>
>
> # But the diagonal doesn't always look the same
>
> heatmap(abs(psim))
>
> # heatmap(abs(psim2))
>
> #####################################
>
>
>
> Thanks!
>
> -Steven Wolf
>
> Lyman Briggs College
>
> Department of Physics and Astronomy
>
> Michigan State University
>
>
> 	[[alternative HTML version deleted]]
>
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