Displaying 5 results from an estimated 5 matches for "sepcolor".
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2007 Dec 16
0
levelplot border and dendrogram width
Hello,
I'm trying to learn how to use lattice and levelplot in particular.
There are three elements of customizing the plots I'm stuck with:
a) Is there a way to put borders around each "cell" within a
level-plot. I'm trying to do something like the
colsep/rowsep/sepcolor/sepwidth parameters of heatmap.2 in gplots
b) Can I alter the line-width of dendrogram added to the levelplot
using latticeExtra?
c) Can I alter the spacing between the dendrogram and a row of
coloured rectanges added to a dendrogram using the add option?
The basic code-example that I've...
2009 Jun 15
0
heatmap.2 questions
I'm using this code to create a heatmap of expression data and indicate a
specific column of data, post clustering:
#Generate heatmap:
heatmapChipDx <- heatmap.2(L3data_med2, dendrogram="column",trace="none",
col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1,
margin=c(5,5), scale="row", key=FALSE)
I have two problems that I'm hoping i can get some pointers on:
1. The column I want to indicate with a yellow line is column #1 in the
matrix, pre-clustering. How can I determine its position post-clustering...
2011 Jul 24
0
setting distance matrix and clustering methods in heatmap.2
...t;Sample 4","Sample 5")
test <- as.table(test)
mat=data.matrix(test)
#pdf("heatmap.pdf", height=10, width=10)
heatmap.2(mat,
dendrogram="row",
Rowv=TRUE,
Colv=NULL,
distfun = dist,
hclustfun = hclust,
xlab = "Lipid Species",
ylab = NULL,
colsep=c(1),
sepcolor="black",
key=TRUE,
keysize=1,
trace="none",
density.info=c("none"),
margins=c(8, 12),
col=bluered
)
--
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Sent from the R help m...
2009 Jul 21
1
problem with heatmap.2 in package gplots generating non-finite breaks
...uot;notecol" "nr"
[49] "op" "retval" "revC" "rm"
[53] "rowInd" "rowsep" "RowSideColors" "Rowv"
[57] "scale" "scale01" "sepcolor" "sepwidth"
[61] "sx" "symbreaks" "symkey" "symm"
[65] "tmpbreaks" "trace" "tracecol" "vline"
[69] "x" "xlab" "x.s...
2009 Jun 15
0
books on Time serie
...m using this code to create a heatmap of expression data and
> indicate a
> specific column of data, post clustering:
>
> #Generate heatmap:
> heatmapChipDx <- heatmap.2(L3data_med2,
> dendrogram="column",trace="none",
> col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1,
> margin=c(5,5), scale="row", key=FALSE)
>
> I have two problems that I'm hoping i can get some pointers on:
>
> 1. The column I want to indicate with a yellow line is column #1 in
> the
> matrix, pre-clustering. How can I det...