]),c(18,63,63,62))
lines(c(barpos$x[1],barpos$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 <r-help@r-project.org> wrote:
> Dear R Community,
> I recently read a
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
with having an open mind is that people 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 <ace...@rocketmail.com> wrote:
Hi, Bert,
Sorry about that! David seemed to be able t
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 regards,
A
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:
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
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
<dwinsem...@comcast.net> wrote:
> On Sep 18, 2017, at 9:2
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
;\t",
col.names=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 <ace...@rocketmail.com> wrote:
> Hi, Jim,
>
> Thank you very much for pointing out
umns with "col.names" and using
"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
<r-help@r-project.org> wrote:
> Dear R community,
> I have a text file (test.txt
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
On Thursday, December 29, 2016 11:44 AM, Ista Zahn <istaz...@gmail.com>
wrote:
Use coord_fixed()
--Ista
On Thu, Dec 29, 2016 at 9:59 AM, Fix Ace via R-help
<r-help@r-project.org> wrote:
>
>
>
> Hello, there,
> What exactly does "expand" do for this fun
.nz> wrote:
>
>
> On 14/02/17 05:50, Fix Ace via R-help wrote:
>
>> 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?
>> Tha
11/02/2017 1:33 PM, Fix Ace via R-help wrote:
> 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"
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"
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 <r-help@r-project.org> wrote:
>
> Hello, there,
> I did a test run for this p
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:
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 +
rid.ls()
The reason why I did my 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
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
ntFill("bwplot.box.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
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
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
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
works. 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 <ace...@rocketmail.com> wrote:
Thank you very much!
I do need to learn more about R!!
On Tuesday, March 17
:
This is really a question about 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
11 3 3
12 3 4
options
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 1
Thank you very much!
I do need to learn more about R!!
On Tuesday, March 17, 2015 9:26 PM, William Dunlap wdun...@tibco.com
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, adjust = 1
wdunlap tibco.com
On Tue, Mar 17, 2015 at 12:06 PM, Fix Ace ace...@rocketmail.com 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$V2), xlim=c(0,1000
I have a dataset with 6187 elements, ranged from 3 to 104028. When I tried to
examine only small range of data, I found that the plot was not smooth (as
shown below):
plot(density(test$V2), xlim=c(0,1000))
Is there away to make it smoother?
Thanks a lot!!
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
z...@dkfz-heidelberg.de wrote:
Hi,
In current version, `labels.font` in `circos.axis` can only be a scalar ( a
vector with length one).
But you can first
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
z...@dkfz-heidelberg.de wrote:
Hi,
In current version, `labels.font` in `circos.axis` can
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,
indices is what you
want) this also works:
m - matrix(1:20,4)
unique(which(m11, arr.ind = T)[,col])
On 27 September 2014 12:23, Jim Lemon j...@bitwrit.com.au 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
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]
.
On Fri, Aug 8, 2014 at 12:25 PM, Fix Ace ace...@rocketmail.com 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� � � � � � � P_5_utr_source_data
� [3] P_exon_per_gene_cds_source_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, 3652765),
+
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
) {
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 ace...@rocketmail.com wrote:
Hello, there,
I have 6
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
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