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Question: Error in plot.new() : figure margins too large
0
gravatar for mictadlo
8 months ago by
mictadlo0
mictadlo0 wrote:

Hi, I have followed this paper but for my data I got the below error:

> #Heat map clustering
> ## ----cpm-----------------------------------------------------------------
> logCPM <- cpm(y, prior.count=2, log=TRUE)
> head(y$genes$genes)
[1] "sp0025247" "sp0025250" "sp0025268" "sp0025270" "sp0025282" "sp0056834"
> y$samples$group
 [1] Root_tip.1.5 Root_tip.1.5 Root_tip.1.5 Root_tip.1.5 Leaves.1.5   Leaves.1.5   Leaves.1.5   Leaves.1.5   Root_tip.2  
[10] Root_tip.2   Root_tip.2   Root_tip.2   Leaves.2     Leaves.2     Leaves.2     Leaves.2     Root_tip.3   Root_tip.3  
[19] Root_tip.3   Root_tip.3   Leaves.3     Leaves.3     Leaves.3     Leaves.3    
Levels: Leaves.1.5 Leaves.2 Leaves.3 Root_tip.1.5 Root_tip.2 Root_tip.3
> rownames(logCPM) <- y$genes$genes
> colnames(logCPM) <- paste(y$samples$group, 1:2, sep="-")
> o <- order(tr$table$PValue)
> logCPM <- logCPM[o[1:30],]
> logCPM <- t(scale(t(logCPM)))
> library(gplots)
> col.pan <- colorpanel(100, "blue", "white", "red")
> heatmap.2(logCPM, col=col.pan, Rowv=TRUE, scale="none",
+           trace="none", dendrogram="both", cexRow=1, cexCol=1.4, density.info="none",
+           mayin=c(10,9), lhei=c(2,10), lwid=c(2,6))
Error in plot.new() : figure margins too large
In addition: Warning messages:
1: In plot.window(...) : "mayin" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "mayin" is not a graphical parameter
3: In title(...) : "mayin" is not a graphical parameter

How is it possible to fix it?

Thank you in advance

ADD COMMENTlink modified 8 months ago by Gordon Smyth33k • written 8 months ago by mictadlo0
2
gravatar for Gordon Smyth
8 months ago by
Gordon Smyth33k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth33k wrote:

You've made a typographical error. The code in the paper says

margin = c(10,9)

but you've entered

mayin = c(10,9)

instead. The error message tells you that "mayin" isn't a correct parameter, so it is easy to see what the problem is.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Gordon Smyth33k
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