Displaying 6 results from an estimated 6 matches for "chr11".
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chr1
2012 Sep 15
2
qplot: plotting precipitation data
...list,
I wish to plot chromatin precipitation data: I would like to have a
rectangles (x:end-start, y:peak) but I do not have an idea how to define x
(in terms of qplot syntax) and to choose the correct geom.
mydata is a subset of a larger file.
> mydata
chrom start end peak
1 chr11 5291000 5291926 8
2 chr11 10988025 10988526 7
3 chr11 11767950 11768676 8
4 chr11 11840900 11841851 8
5 chr11 12267450 12268076 12
6 chr11 12276675 12277051 7
> dput(mydata)
structure(list(chrom = structure(c(3L, 3L, 3L, 3L, 3L, 3L), .Label =
c("chr1",
"chr10&qu...
2008 Nov 26
1
Smoothed 3D plots
...0, 2, 1,
2, 0, 1, 2, 2, 2, 0, 1, 1, 0, 0, 0)), .Names = c("y", "h4",
"h11"), class = "data.frame", row.names = c(NA, -28L))
# ------------
# Some plots
# ------------
# Option 1
require(Rcmdr)
with(res,
scatter3d(h4,ypred,h11, xlab='Chr4',zlab='Chr11',
ylab='Ratio',fit=c("linear","quadratic"))
)
# Option 2
require(scatterplot3d)
with(res,
scatterplot3d(h4,ypred,h11, xlab='Chr4',zlab='Chr11',ylab='Ratio')
)
# -------------
# Session info
# -------------
R version 2.8.0 Patched (2008-11-0...
2010 Nov 07
1
How do I order xyplot line points?
...follows:
Type Elements Chromosome Time
bedGz 12000000 chr1 14.240
bedGz 12000000 chr2 7.949
bedGz 12000000 chr3 5.103
bedGz 12000000 chr4 5.290
bedGz 12000000 chr5 5.161
...
The x-axis labels in the Chromosome column are ordered lexicographically in my figure ( chr1 > chr10 > chr11 > ... ) ? this is correct.
However, the code I use to draw lines between points in the xyplot connects points in numerical order ( chr1 > chr2 > ... ) ? this is incorrect.
The problem this causes is most evident in the line that is drawn for the blue "bedGz" category.
What I...
2012 Jun 21
2
Simple Question?
...er" using ggplot2.
I have data.frame that contains
chrom length
1 chr1 249250621
2 chr2 243199373
3 chr3 198022430
4 chr4 191154276
5 chr5 180915260
6 chr6 171115067
7 chr7 159138663
8 chrX 155270560
9 chr8 146364022
10 chr9 141213431
11 chr10 135534747
12 chr11 135006516
13 chr12 133851895
14 chr13 115169878
15 chr14 107349540
16 chr15 102531392
17 chr16 90354753
18 chr17 81195210
19 chr18 78077248
20 chr20 63025520
21 chrY 59373566
22 chr19 59128983
23 chr22 51304566
24 chr21 48129895
I want to drop the "chr" and order th...
2011 Jul 27
2
Writing a summary file in R
Hello,
I have an input file:
http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt
where col 1 is chromosome, column2 is start of region, column 3 is end of
region, column 4 and 5 is base position, column 6 is total reads, column 7
is methylation data, and column 8 is the strand.
I would like a summary output file such as:
2011 Apr 15
1
Whole genome searching of 100bp "D" sequence
...DDDDDDDDDDDDDDDD") #
60bp C free sequence
query.minus <- reverseComplement(query.plus)
chrList <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16",
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")
#access/group the by subset of annotation
anno...