Displaying 11 results from an estimated 11 matches for "colsep".
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colse
2011 Sep 21
0
heatmap.2 with colsep and sepwidth
I am using attributes colsep and sepwidth from heatmap.2 function,
however when using larger values for sepwidth the following columns are
not moved to the right but the seperator is covering the column(s) with
a white bar and the column labels and ColSideColors remain at their
positions, is this intended? I expected the f...
2004 Sep 07
1
gridBase and heatmap
...ewport[GRID.VP.178]
> par(omi=gridOMI(),new=T)
> my.heatmap(eb$coefficients[(clsum[,1]>1) & (clsum[,2]>1) &
(clsum[,3]==0),],breaks=c(seq(-2.5,-0.6,0.1),
-0.1,0.10,seq(0.6,2.5,0.1)),dendrogram="none",Colv=c(9:12,5:8,1:
4),labRow=rep('',520),margin=c(10,5),colsep=c(4,8),trace="none",density.
info="none",col=greenred.colors(40),key=F)
> popViewport()
viewport[GRID.VP.177]
> pushViewport(viewport(layout.pos.col=3))
viewport[GRID.VP.179]
> pushViewport(viewport(layout = grid.layout(3, 1, heights =
unit(rep(1,3), c("null&...
2017 Jun 17
3
write.dna command
...DNAid <- "JF806202"
# Store the sequence in lst (a list)
lst <- read.GenBank(DNAid, as.character = T)
# convert the sequence to fasta format
write.dna (lst, file = "DNAseq.fasta", format = "fasta", append =
FALSE,
nbcol= 6, colsep= " ", colw= 10)
Any help will be appreciated.
Thank you.
Kelas
[[alternative HTML version deleted]]
2017 Jun 17
0
write.dna command
...quot;
>
> # Store the sequence in lst (a list)
> lst <- read.GenBank(DNAid, as.character = T)
>
> # convert the sequence to fasta format
> write.dna (lst, file = "DNAseq.fasta", format = "fasta", append =
>FALSE,
> nbcol= 6, colsep= " ", colw= 10)
>
>
>Any help will be appreciated.
>Thank you.
>
>Kelas
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.c...
2006 Feb 02
0
Heatmap.2 axes question
...o
effect. My complete code is:
hv <- heatmap.2(hmrf, Rowv=1:nrow(hmrf), Colv=1:ncol(hmrf), symm=TRUE,
margin=c(6, 6), trace="none", col=terrain.colors(256),
main = "Heatmap: Respondent Proximities", tracecol="red",
dendrogram="none", colsep=c(398, 811),
rowsep=c(398, 811), labRow = " ", labCol = " ")
axis(1, at=seq(500, 1000, 500))
mtext("Group 1", "Group 2")
Note: I'm preventing re-ordering so that observations within groups are
adjacent to one another. Th...
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-examp...
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...
2011 Jul 24
0
setting distance matrix and clustering methods in heatmap.2
...3", "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
)
--
View this message in context: http://r.789695.n4.nabble.com/setting-distance-matrix-and-clustering-methods-in-heatmap-2-tp3690173p3690173.html
Sent fr...
2009 Jul 21
1
problem with heatmap.2 in package gplots generating non-finite breaks
...owse[1]> heatmap.func.R
Error during wrapup: object 'heatmap.func.R' not found
Browse[1]> ls()
[1] "add.expr" "breaks" "cellnote" "cexCol"
[5] "cexRow" "col" "colInd" "colsep"
[9] "ColSideColors" "Colv" "ddc" "ddr"
[13] "dendrogram" "densadj" "denscol" "density.info"
[17] "di" "distfun" "hcc" &qu...
2015 Jul 21
2
glm com etiquetas en las variables
Hola:
Si aún hay alguien que no está de vacaciones, igual me pueden ayudar.
Quiero ajustar unos modelos:
REG_LOG <- glm (low ~ X, family = "binomial", data = DATOS)
Ejemplo:
library(MASS)
data(birthwt, package="MASS")
birthwt$low <- factor(birthwt$low)
birthwt$race <- factor(birthwt$smoke)
REG_LOG <- glm (low ~ smoke, family =
2009 Jun 15
0
books on Time serie
...;
> 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...