I want to represent a histogram by the line along its top border, *without*
kernel smoothing (to show several histograms in the same plot). This works,
but is there simpler recommended way?
x - rnorm(1000)
tmp - hist(x, border=white)
for (i in 1:(length(tmp$breaks)-1)){
Very nice - thank you, I didn't know about type='s'.
On Thu, Aug 1, 2013 at 3:43 PM, Greg Snow 538...@gmail.com wrote:
lines( tmp$breaks, c(tmp$counts,tail(tmp$counts,1)), type='s',
col='#00ff0077', lwd=5 )
On Thu, Aug 1, 2013 at 1:30 PM, Levi Waldron
lwaldron.resea...@gmail.comwrote
Perhaps I am wrong, but I think there are only a few packages supporting
Elastic Net, and none of them also perform Best Subsets.
On Wed, Apr 17, 2013 at 8:46 AM, Christos Giannoulis cgiann...@gmail.comwrote:
Merhaba, Hello to you too Mehmet (Yasu ki sena)
Thank you for your email and
For posterity, I found the TeachingDemos::shadowtext option most
agreeable for this problem:
* legend puts a large box around the text which did not seem
possible to shrink, and does not accept vector x, y arguments
* plotrix::boxed.labels did not work with pos=4 (this moved the
text, but
I would like to draw horizontal or vertical lines on a heatmap to
highlight the clusters at some specified cut depth of the dendrogram.
As a hacked example, the following code would work if I could set the
coordinates of the top and bottom of the false color image correctly
(ymin and ymax), but
Is there a logic to this difference, or is it just a quirk of the history of
these functions?
I found one discussion on this topic, but without what I thought was a very
conclusive end:
http://finzi.psych.upenn.edu/Rhelp08/2009-March/191930.html
--
Levi Waldron
post-doctoral fellow
Jurisica Lab
://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
(416)581-7453
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Levi Waldron
post-doctoral fellow
Jurisica Lab
() #as per example code
par(mfrow=c(2,1))
makeplot()
makeplot()
par(mfrow=c(1,2))
makeplot()
makeplot()
dev.off()
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
(416)581-7453
(xpos),label=y=x,pos=3)
par(srt=g_angle)
text(xpos,g(xpos),label=y=2x,pos=3)
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
(416)581-7453
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then gets you to ?plot (actually plot.default() )
Bert Gunter
Genentech Nonclinical Biostatisics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On
Behalf Of Levi Waldron
Sent: Thursday, August 27, 2009 1:54 PM
To: r-help@r-project.org
Subject
)
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
(416)581-7453
[[alternative HTML version deleted]]
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R-help@r-project.org mailing
like to
put all three annotations on the heatmap by putting three rows of +/- values
between the top of the heatmap and the dendrogram, or even three colored
bars. Specific or general suggestions would be welcome.
Thank you,
Levi
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario
Perhaps:
gc()
On Wed, Mar 18, 2009 at 8:26 AM, Abelian abelian1...@gmail.com wrote:
Dear all
when the program is runing, we can realize that the memory size will
be asked more and more..
Therefore, we could meet the significant problem, such as out off
memory size.
However, even if i
Your first example that works would just repeat the atomic vector to the
length of the row. To replace a row with another data frame, you could use
rbind:
avGain - rbind(avGain[-j,],b)
Or if the positioning is important,
2) avGain - rbind(avGain[1:(j-1),],b,avGain[(j+1):nrow(avGain),])
I
()?
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
IBM Life Sciences Discovery Centre
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
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R
On Tue, Mar 17, 2009 at 12:56 PM, Patrick Burns pbu...@pburns.seanet.comwrote:
Use 'do.call' as discussed in 'The R Inferno'
and elsewhere.
Perfect, thanks.
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
IBM Life Sciences Discovery
it sounds like you've
figured out.
cheers,
Levi
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
IBM Life Sciences Discovery Centre
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
[[alternative HTML version deleted
=)))
a1 a2 a3 a4 b1 b2 b3 c1 c2d
ab ac ad ae bc bd be cd ce de
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
IBM Life Sciences Discovery Centre
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
I like both of these solutions much better - thank you!
-Levi
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
IBM Life Sciences Discovery Centre
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
) - c(ResultA, ResultB, ResultC) return(results)
}
variables - sapply(filenames,docalc)
--
Levi Waldron
post-doctoral fellow
Jurisica Lab, Ontario Cancer Institute
Division of Signaling Biology
IBM Life Sciences Discovery Centre
TMDT 9-304D
101 College Street
Toronto, Ontario M5G 1L7
(416)581
This one should be easy but it's giving me a hard time mostly because tapply
puts the results in a list. I want to calculate the cumulative sum of a
variable in a dataframe, but with the accumulation only within each level of
a factor. For a very simple example, take:
df -
Perfect, thanks all. Unlist and ave will both be very handy functions to
know. -levi
--
Levi Waldron, PhD
Treated Wood Research Group
Faculty of Forestry, University of Toronto
33 Willcocks Street, Toronto ON, M5S 3B3 CANADA
Tel 647-866-5384
Fax 416-978-3834
[[alternative HTML
a bootstrap method, or
something else?
ps. the data is attached to the end of this email.
On Thu, Jun 5, 2008 at 6:25 PM, Levi Waldron [EMAIL PROTECTED] wrote:
I am trying to model the observed leaching of wood preservative chemicals
from treated wood during an outdoor experiment where leaching
Here's a simple example:
x - 1:5
plot(x,x^2)
lines(x,x^2)
points(x,x,cex=2)
lines(x,x,lw=3)
legend(topleft,legend=c(y=x^2,y=x),pch=1,pt.cex=1:2,lw=c(1,3))
The thickness of the circles in the legend changes with lw. If you change
the lw argument in legend to lw=c(1,1) then the thickness of the
I am wondering how to customize a pairwise comparisons plot of a factorial
ANOVA, without doing a lot of manual manipulation of a TukeyHSD object. The
customizations I'd like are:
1. The aov used log-transformed response data, but I'd like to plot the
intervals on their original, untransformed
I'm interested in restricting the pairwise comparisons of interaction
effects in a multi-way factorial ANOVA, because I find comparisons of
interactions between all different variables different to interpret.
For example (supposing a p0.10 cutoff just to be able to use this
example):
summary(fm1
Using the following lattice plot as an example, I would like to add
horizontal lines where y=0:
library(lattice)
library(grid)
fac - gl(4,12)
x - letters[rep(1:3,16)]
y - runif(48,min=0.0)
dotplot(y~x|fac)
I've tried it with grid.lines using npc and native units, which works
fine unless I change
*Thank you* Greg, this function works perfectly! I had imagined that
the ideal solution would iteratively modify the vector to fix new
violations of mindiff created by each subsequent spreading of tight
clusters, but couldn't figure how to do it. A small note, the vector
x must be sorted before
Would this function be worth submitting to some existing cran library?
I'd be willing to document it and add error-checking if there is
somewhere that it belongs (with credit to Greg of course, unless Greg
wants to submit it himself).
I am using it in conjunction with a function I wrote which
I am creating a timeline plot, but running into a problem in positions
where the values to plot are too close together to print the text
without overlap. The simplest way I can think of to solve this
(although there may be other ways?) is to create a new numeric vector
whose values are as close
On Sat, Mar 22, 2008 at 9:58 PM, jim holtman [EMAIL PROTECTED] wrote:
Is this close to what you want?
spread - function(x, mindiff=0.5){
+ unique(as.integer(x / mindiff) * mindiff)
+ }
x - c(1,2,seq(2.1,2.3,0.1),3,4)
x
[1] 1.0 2.0 2.1 2.2 2.3 3.0 4.0
spread(x)
[1] 1 2
What functions exist for differentiating a numeric vector (in my case
spectral data)? That is, experimental data without an analytical
function. ie,
x - seq(1,10,0.1)
y=x^3+rnorm(length(x),sd=0.01) #although the real function would be
nothing simple like x^3...
derivy -
I know I
I have a dataframe with several different treatment variables, and
would like to calculate the mean and standard deviation of the
replicates for each day and treatment variable. It seems like it
should be easy, but I've only managed to do it for one treatment at a
time using subset and tapply.
On Tue, Mar 4, 2008 at 5:32 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
Try this:
library(doBy)
summaryBy(. ~ day + treat, exampledata, FUN = c(mean, sd))
Outstanding, so much better. Thanks.
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