Hi, Dr. Gu,
I am trying to highlight some axis labels, for example, "72hL3" as bold, using
the following command:
circos.initialize(factors=female.f, xlim=c(1.8,6.2))
circos.trackPlotRegion(factors=female.f,
ylim=c(-1.3,1.8),track.height=0.5,panel.fun=function(x,y){circos.axis(major.at=c(2:6),mi
I was trying to ask if there is way to change the color of the axis...
Thanks!
On Monday, December 15, 2014 1:39 PM, "Gu, Zuguang"
wrote:
Hi,
In current version, `labels.font` in `circos.axis` can only be a scalar ( a
vector with length one).
But you can first add axes with no labe
Hi, Dr. Gu,
Thank you very much for the answer. This trick works.
Another question, is there a way to change the color or the axis?
Thanks!
On Monday, December 15, 2014 1:39 PM, "Gu, Zuguang"
wrote:
Hi,
In current version, `labels.font` in `circos.axis` can only be a scalar ( a
v
I have a dataset with 6187 elements, ranged from 3 to 104028. When I tried to
examine only small range of data, I found that the plot was not smooth (as
shown below):
plot(density(test$V2), xlim=c(0,1000))
Is there away to make it smoother?
Thanks a lot!!
___
re
wdunlap tibco.com
On Tue, Mar 17, 2015 at 12:06 PM, Fix Ace wrote:
I have a dataset with 6187 elements, ranged from 3 to 104028. When I tried to
examine only small range of data, I found that the plot was not smooth (as
shown below):
plot(density(test$V2), xlim=c(0,1000))
Is there away
Thank you very much!
I do need to learn more about R!!
On Tuesday, March 17, 2015 9:26 PM, William Dunlap
wrote:
Fix Ace wrote What is the default "n"?
512: > length(density(rnorm(10^6))$x) [1] 512 > args(density.default)
function (x, bw = "nrd0&quo
I tried to run the sample code from R:
dd <- data.frame(a = gl(3,4), b = gl(4,1,12)) a b
1 1 1
2 1 2
3 1 3
4 1 4
5 2 1
6 2 2
7 2 3
8 2 4
9 3 1
10 3 2
11 3 3
12 3 4
options("contrasts")
model.matrix(~ a + b, dd)(Intercept) a2 a3 b2 b3 b4
11 0 0 0 0 0
21 0 0
statistics rather than R but see below
On 01/04/2015 06:28, Fix Ace wrote:
> I tried to run the sample code from R:
> dd <- data.frame(a = gl(3,4), b = gl(4,1,12)) a b
> 1 1 1
> 2 1 2
> 3 1 3
> 4 1 4
> 5 2 1
> 6 2 2
> 7 2 3
> 8 2 4
> 9 3 1
> 10 3 2
Hello, there,
I have 6 dataset and trying to draw a venn.diagram using R VennDiagram package,
but got this error message. Could anybody figure out why?
Thanks
===
> library(VennDiagram)
Loading required package: grid
> head(A)
V1
1 F_HO1
2 F_HO10001
3 F_HO10002
4 F_HO10003
5 F
stop("Incorrect number of elements.", call. = FALSE)
}
If you really need 6, you could presumably look at the way that
venn.diagram() works and add in your own 6-handling code.
Sarah
On Tue, Jul 29, 2014 at 11:11 AM, Fix Ace wrote:
> Hello, there,
> I have 6 data
I recently tried to run some sample code from R package: circlize,
and got an error message (please see below) = > library(circlize) >
circos.genomicInitialize(df) > df = data.frame(name = c("TP53", "TP63",
"TP73"), + start = c(7565097, 189349205, 3569084),
+ end = c(7590856, 189615068, 3652
I have 16 files and would like to check the information of their first two
lines, what I did:
> ls(pattern="P_")
[1] "P_3_utr_source_data" "P_5_utr_source_data"
[3] "P_exon_per_gene_cds_source_data" "P_exon_per_gene_source_data"
[5] "P_exon_source_data"
as well in a simpler way
than looping.
On Fri, Aug 8, 2014 at 12:25 PM, Fix Ace wrote:
> I have 16 files and would like to check the information of their first two
> lines, what I did:
>
>
>> ls(pattern="P_")
>� [1] "P_3_utr_source_data"� � �
Hello, there,
I wonder if there is an easier way that I would only get the rows that
satisfies some condition. For example:I have the following matrix, and I would
like to output only the 3rd row and 4th row, since only these two rows contain
the numbers greater than 11
> a
[,1] [,2] [,3] [
) this also works:
m <- matrix(1:20,4)
unique(which(m>11, arr.ind = T)[,"col"])
On 27 September 2014 12:23, Jim Lemon wrote:
> On Fri, 26 Sep 2014 10:15:14 PM Fix Ace wrote:
>> Hello, there,
>> I wonder if there is an easier way that I would only get the rows that
&
Hello, there,
I will like to fill the boxplot with gradient color, as exampled below:
Can anyone help me figure out what package I should go with?
Thank you very much for any inputs!
Kind regards,
Ace
__
R-help@r-project.org mailing list -- To UNSUBSCRIB
Dear R Community,
Is there a way to adjust the line width of the dendrogram in heat map.2
function? I tried "lwd", but it didn't work...
Also, is there a way to adjust the general height/width/position of the
dendrogram using heatmap.2 function? I feel the portion of the dendrogram is
huge compa
Dear R Community,
My data have 3 conditions and each condition has 6 replicates. I am trying to
fit my data for a linear mixed model using the lmer function from lme4 package
to find the random effects of the replicates; however, I got the error message.
Here are the example codes:
>example.3=da
m effects (=18) for term
> (conditions | replicate); the random-effects parameters and the residual
> variance (or scale parameter) are probably unidentifiable>
Please let me know if it is readable this time.
Again, many thanks for your time and please help me fix the issue.
Kind rega
eople keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Wed, Nov 15, 2017 at 5:09 AM, Fix Ace wrote:
Hi, Bert,
Sorry about that! David seemed to be able to read the post since he replied.
Here I just email you
Dear R Community,
I recently read an article and found a plot as attached. It has scatterplot,
barplot, and error bar. Could anyone help me to figure out what package I can
use in R to generate such plot?
Thank you very much for any inputs!
Kind regards,
Ace
__
arpos$x[1],barpos$x[1],barpos$x[3],barpos$x[3]),c(4,66,66,65))
text(2,68,"**",cex=2)
text(2.5,64.5,"**",cex=2)
Jim
On Mon, Feb 5, 2018 at 8:56 AM, Fix Ace via R-help wrote:
> Dear R Community,
> I recently read an article and found a plot as attached. It has scatterplo
On Thursday, December 29, 2016 11:44 AM, Ista Zahn
wrote:
Use coord_fixed()
--Ista
On Thu, Dec 29, 2016 at 9:59 AM, Fix Ace via R-help
wrote:
>
>
>
> Hello, there,
> What exactly does "expand" do for this function?
> I followed the examples from the manual to
Dear R community,
I have a text file (test.txt) with different number of columns:
0610007P14Rik%%% Tcf19 Gtf2i 0610010O12Rik%%% Ivns1abp Etv6 111G20Rik%%%
Nmi 1500015O10Rik%%% Foxi1 Ascl3 Sirt3 173E16Rik%%% Ascl2 Ifnar2
1700028J19Rik%%% Musk Nfe2l3 1810011O10Rik%%% Ppp1r13b Bpnt1 Cdkn2c F
ing
"fill=TRUE" you can get a data frame with zero length strings where
values are missing in the input file.
Jim
On Mon, Aug 28, 2017 at 6:25 AM, Fix Ace via R-help
wrote:
> Dear R community,
> I have a text file (test.txt) with different number of columns:
> 0610007
ames=paste("V",1:19,sep=""),stringsAsFactors=FALSE)
Also note that I got the number of columns wrong the first time.
Jim
On Mon, Aug 28, 2017 at 12:56 PM, Fix Ace wrote:
> Hi, Jim,
>
> Thank you very much for pointing out the format issue. Here is the original
> text:
>
&
Dear R community,
I would like to plot a partial hclust output, so I am looking for a subtree
function that would return an tree structure I can plot.
I ran the test code of subtree following the instruction on
http://finzi.psych.upenn.edu/library/extracat/html/subtree.html
However, an error mess
Thank you so much for the reply! I thought the file would automatically adjust
accordingly. But I just checked and found pheatmap does has width as parameter!
Ace
On Monday, September 18, 2017 3:00 PM, David Winsemius
wrote:
> On Sep 18, 2017, at 9:26 AM, Fix Ace via R-help wr
ks. However, when I tried: grep(z|v,a), it did not
work. Can anyone help how to handle such situation?
Thanks.
Ace
On Wednesday, March 18, 2015 5:52 PM, Fix Ace wrote:
Thank you very much!
I do need to learn more about R!!
On Tuesday, March 17, 2015 9:26 PM, William Dunlap
wrote:
Hello, there,
R document for heatmap says that Rowv could be a vector of values to specify
the row order. However, I couldn't figure out how to apply it. A simple example
here:> b=as.data.frame(matrix(c(3,4,5,8,9,10,13,14,15,27,19,20),3,4))
> b
V1 V2 V3 V4
1 3 8 13 27
2 4 9 14 19
3 5 10 15
Hello, there,
R document for heatmap says that Rowv could be a vector of values to specify
the row order. However, I couldn't figure out how to apply it. A simple example
here:> b=as.data.frame(matrix(c(3,4,5,8,9,10,13,14,15,27,19,20),3,4))
> b
V1 V2 V3 V4
1 3 8 13 27
2 4 9 14 19
3 5 10 15
polygon", label=rep("br", 17), grep=TRUE,
group=FALSE)
# Generate SVG version "Rplots.svg"
# (where the gradient will actually be visible)
grid.export()
Does that help ?
Paul
On 07/12/16 09:14, Fix Ace wrote:
> Hello, there,
> I will like to fill t
Hi, Paul,
Thank you very much! It works this time with "strict=FALSE" option.
Another relevant question:
how did you figure out that boxes in boxplot are called "bwplot.box.polygon".
If I am trying to make a gradient filling for barplot of other plots, how would
I define grobs?
Thanks!!
Ace
example using 'lattice' is because 'lattice'
names all of its grobs. There is a document ...
http://lattice.r-forge.r-project.org/Vignettes/src/naming-scheme/namingScheme.pdf
... that describes the 'lattice' naming scheme.
Paul
On 10/12/16 10:39, Fix Ace wrote:
Hello, there,
What exactly does "expand" do for this function?
I followed the examples from the manual to get a plot:
d <- ggplot(subset(diamonds, carat > 1), aes(cut, clarity)) +geom_jitter()
I would like to have all the dots in a square instead of rectangular range.
When I applied d + sca
Hello, there,
I did a test run for this princomp() function using USArrests data. The R
document says that the output loadings contain the eigenvector matrix. When I
looked at this matrix, I found that a missing item for Comp.4
> p3=princomp(USArrests, cor=TRUE )> p3$loadings
Loadings:
Comp.1 Comp.2 Comp.3 Comp.4
SS loadings 1.00 1.00 1.00 1.00
Proportion Var 0.25 0.25 0.25 0.25
Cumulative Var 0.25 0.50 0.75 1.00
Cheers,
Ben
> On Jan 29, 2017, at 4:31 AM, Fix Ace via R-help wrote:
>
> Hello, there,
> I did a test run for this princom
Hello, there,
I wrote a loop to check the dimension of all the .txt dataframes:> ls()
[1] "actualpca.table" "b4galnt2" "b4galnt2.txt" "data"
[5] "galnt4" "galnt4.txt" "galnt5" "galnt5.txt"
[9] "galnt6" "galnt6.txt" "glyco" "glyco.txt"
[13]
Well, I am not trying to print anything. I just would like to get the dimension
information for all the dataframes I created. Could you please help me to
develop the script?
Thanks.
Ace
On Saturday, February 11, 2017 7:53 PM, Duncan Murdoch
wrote:
On 11/02/2017 1:33 PM, Fix Ace via R
ad of the for loop, but even better is to store each of your
objects in a list as you create them rather than letting them get loose in the
global environment. That way you don't have to do this get-by-name rodeo to
get info on them.
Cheers,
Ben
> On Feb 14, 2017, at 2:57 AM, Rolf T
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