Re: [R] need help with distribution graphics
Thanks a lot! On Saturday, December 28, 2013 2:54 PM, Jim Lemon j...@bitwrit.com.au wrote: On 12/29/2013 03:41 AM, capricy gao wrote: Really? OK, here the linked is an example: http://iai.asm.org/content/77/10/4631/F1.expansion.html Please, any input would be appreciated! Hi Capricy, Really. Try the beeswarm package or the ehplot or dendroPlot functions in the plotrix package. Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] need help with distribution graphics
Really? OK, here the linked is an example: http://iai.asm.org/content/77/10/4631/F1.expansion.html Please, any input would be appreciated! On Saturday, December 28, 2013 6:28 AM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 28.12.2013 04:25, capricy gao wrote: I need to graph categorical data like a or b in the the following figure. Could anybody let me know what command line I should go with? Figures are removed when this goes to the mailing list, so nobody knows what you are talking about. Better provide a link to some web resource. Best, Uwe Ligges Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] need help with distribution graphics
I need to graph categorical data like a or b in the the following figure. Could anybody let me know what command line I should go with? Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] hist() : is there a way to change the border width?
Thanks a lot. It works! On Thursday, December 19, 2013 10:53 PM, Jim Lemon j...@bitwrit.com.au wrote: On 12/20/2013 08:19 AM, capricy gao wrote: I have played around with it and found that the only color could be changed. But I really would like to change the width... Hi Capricy, Try this on the first example for hist: hist(islands) par(lwd=3) hist(islands) Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] hist() : is there a way to change the border width?
I have played around with it and found that the only color could be changed. But I really would like to change the width... Thanks a lot :) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot() function: color transparency
I found all the color transparency was defined with character color, or rgb color. What if I have number code and still try to modify the transparency? For example: x=c(1:5) color=c(2,2,3,4,5) plot(x, col=color) plot(x, col=color,pch=20) here I defined color by numbers, how can I modify the transparency? Thanks a lot for any input! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot() function: color transparency
I checked as you suggested. However, I found that the number in those functions are the number of colors. In contrast, my number here means a specific color, for example, 2 in my code means red, 3 in my code means green On Wednesday, December 18, 2013 1:18 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-12-18 2:08 PM, capricy gao wrote: I found all the color transparency was defined with character color, or rgb color. What if I have number code and still try to modify the transparency? For example: x=c(1:5) color=c(2,2,3,4,5) plot(x, col=color) plot(x, col=color,pch=20) here I defined color by numbers, how can I modify the transparency? See the examples for ?palette. Duncan Murdoch [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Heatmap, and heatmap.2 gave different figures for the same dataset
I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: dim(as.matrix(data.dcpm)) [1] 15462 18 heatmap(as.matrix(data.dcpm), col=topo.colors(100)) heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE, density.inf=none,trace=none, scale=none) --- The outputs are attached here. Could anyone help me figure out why? Thanks a lot:) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] method default for hclust function
I could not figure out what was the default when I ran hclust() without specifying the method. For example: I just have a code like: hclust(dist(data)) Any input would be appreciated:) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Heatmap, and heatmap.2 gave different figures for the same dataset
Thank you very much for the hints. I fixed the problem. On Thursday, December 12, 2013 2:08 PM, Kevin Wright kw.s...@gmail.com wrote: Read the help page for both and pay particular attention to the scale argument. Kevin Wright On Thu, Dec 12, 2013 at 9:45 AM, capricy gao capri...@yahoo.com wrote: I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: dim(as.matrix(data.dcpm)) [1] 15462 18 heatmap(as.matrix(data.dcpm), col=topo.colors(100)) heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE, density.inf=none,trace=none, scale=none) --- The outputs are attached here. Could anyone help me figure out why? Thanks a lot:) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Kevin Wright [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with grep under loop
Thanks a lot. It works great now!
Cc: R help r-help@r-project.org
Sent: Friday, September 13, 2013 11:46 PM
Subject: Re: [R] problem with grep under loop
Hi,
dat1- read.table(gao.txt,sep=,header=FALSE,stringsAsFactors=FALSE)
dat1
# V1 V2 V3 V4 V5 V6 V7 V8
#1 ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo
#2 - - u C.3 C.3.1 100 1.00 0.00
#3 - - u C.2 C.2.1 100 1.00 0.00
#4 - - u C.4 C.4.1 100 1.00 0.00
#5 - - u C.1 C.1.1 100 1.00 0.00
#6 - - u C.5 C.5.1 100 1.00 0.00
# V9 V10 V11 V12 V13
#1 FPKM_conf_hi cov len major_iso_id ref_match_len
#2 0.00 0.056682 96 C.3.1 -
#3 0.00 0.058453 99 C.2.1 -
#4 0.00 0.059634 101 C.4.1 -
#5 0.00 0.059634 101 C.2.1 -
#6 0.00 0.059634 101 C.5.1 -
You should read the dataset with read.table(, header=TRUE) as your dataset
already had colnames.
for(i in 1:nrow(dat1)){if(length(grep(dat1[i,4],dat1[i,12])==1)!=0) print(Y)}
[1] Y
[1] Y
[1] Y
[1] Y
A.K.
Sorry about that. I will try to reformat my question.
I have a dataset with format like:
--
head(data)
V1 V2 V3 V4 V5 V6 V7 V8
1 ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo
2 - - u C.3 C.3.1 100 1.00 0.00
3 - - u C.2 C.2.1 100 1.00 0.00
4 - - u C.4 C.4.1 100 1.00 0.00
5 - - u C.1 C.1.1 100 1.00 0.00
6 - - u C.5 C.5.1 100 1.00 0.00
V9 V10 V11 V12 V13
1 FPKM_conf_hi cov len major_iso_id ref_match_len
2 0.00 0.056682 96 C.3.1 -
3 0.00 0.058453 99 C.2.1 -
4 0.00 0.059634 101 C.4.1 -
5 0.00 0.059634 101 C.7.1 -
6 0.00 0.059634 101 C.5.1 -
-
here column5 has extra .1 compared with column4, and column12
might be different from column5 with similar format, for example row 5;
but most of them (column5 and column12) are the same (like the rest of
the rows) . I am trying to find the different ones by using grep
this data has a dimension of 52086 by 13
so my ran the following code:
dim(data)
[1] 52086 13
if(grep(data[3,4],data[3,12])==1) print(Y)
[1] Y
for(i in 1:52086){if(grep(data[i,4],data[i,12])==1) print (Y)}
Error in if (grep(data[i, 4], data[i, 12]) == 1) print(Y) :
argument is of length zero
---
here I tested the grep command first and it looks ok. However, when I put it in
for loop, error message came:
argument is of length zero
Could you please help me figure out what happened here?
Thanks a lot for your help.
- Original Message -
To: r-help@r-project.org r-help@r-project.org
Cc:
Sent: Friday, September 13, 2013 9:29 PM
Subject: [R] problem with grep under loop
I am just testing the possibility of using grep under for loop:
for(i in 1:10){grep(a,letters)}
nothing came out;
when I ran:
grep(a,letters),
I got 1
so in my for loop, I expected to see ten 1s, but I did not.
Could anybody help me to figure out why? Thanks a lot for your help.
Capricy
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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R-help@r-project.org mailing list
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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.
[R] problem with grep under loop
I am just testing the possibility of using grep under for loop:
for(i in 1:10){grep(a,letters)}
nothing came out;
when I ran:
grep(a,letters),
I got 1
so in my for loop, I expected to see ten 1s, but I did not.
Could anybody help me to figure out why? Thanks a lot for your help.
Capricy
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with grep under loop
Thanks a lot for all the responses!!
I then first test my data:
dim(data)
[1] 52086 13
if(grep(data[3,4],data[3,12])==1) print(Y)
[1] Y
for(i in 1:52086){if(grep(data[i,4],data[i,12])==1) print (Y)}
Error in if (grep(data[i, 4], data[i, 12]) == 1) print(Y) :
argument is of length zero
What is this new error message? argument is of length zero
Here is my data format:
head(data)
V1 V2 V3 V4 V5 V6 V7 V8
1 ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo
2 - - u C.3 C.3.1 100 1.00 0.00
3 - - u C.2 C.2.1 100 1.00 0.00
4 - - u C.4 C.4.1 100 1.00 0.00
5 - - u C.1 C.1.1 100 1.00 0.00
6 - - u C.5 C.5.1 100 1.00 0.00
V9 V10 V11 V12 V13
1 FPKM_conf_hi cov len major_iso_id ref_match_len
2 0.00 0.056682 96 C.3.1 -
3 0.00 0.058453 99 C.2.1 -
4 0.00 0.059634 101 C.4.1 -
5 0.00 0.059634 101 C.2.1 -
6 0.00 0.059634 101 C.5.1 -
From: Jeff Newmiller jdnew...@dcn.davis.ca.us
h...@r-project.org r-help@r-project.org
Sent: Friday, September 13, 2013 9:21 PM
Subject: Re: [R] problem with grep under loop
This is because you are not printing it (with the print or cat functions). Keep
in mind that the visible result you get from calling a function or evaluating a
variable interactively comes from the interactive R command line, not from R
itself. Once you put such an expression inside a function (such as the for
function) it is no longer directly being invoked by the command interpreter.
You might want to read [1] and [2] (which says don't post using HTML).
[1]
http://stackoverflow.com/questions/4716152/why-do-r-objects-not-print-in-a-function-or-a-for-loop
[2] http://www.R-project.org/posting-guide.html
---
Jeff Newmiller The . . Go Live...
DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
I am just testing the possibility of using grep under for loop:
for(i in 1:10){grep(a,letters)}
nothing came out;
when I ran:
grep(a,letters),
I got 1
so in my for loop, I expected to see ten 1s, but I did not.
Could anybody help me to figure out why? Thanks a lot for your help.
Capricy
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with grep under loop
Sorry about that. I will try to reformat my question.
I have a dataset with format like:
--
head(data)
V1 V2 V3 V4 V5 V6 V7 V8
1 ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo
2 - - u C.3 C.3.1 100 1.00 0.00
3 - - u C.2 C.2.1 100 1.00 0.00
4 - - u C.4 C.4.1 100 1.00 0.00
5 - - u C.1 C.1.1 100 1.00 0.00
6 - - u C.5 C.5.1 100 1.00 0.00
V9 V10 V11 V12 V13
1 FPKM_conf_hi cov len major_iso_id ref_match_len
2 0.00 0.056682 96 C.3.1 -
3 0.00 0.058453 99 C.2.1 -
4 0.00 0.059634 101 C.4.1 -
5 0.00 0.059634 101 C.7.1 -
6 0.00 0.059634 101 C.5.1 -
-
here column5 has extra .1 compared with column4, and column12 might be
different from column5 with similar format, for example row 5; but most of them
(column5 and column12) are the same (like the rest of the rows) . I am trying
to find the different ones by using grep
this data has a dimension of 52086 by 13
so my ran the following code:
dim(data)
[1] 52086 13
if(grep(data[3,4],data[3,12])==1) print(Y)
[1] Y
for(i in 1:52086){if(grep(data[i,4],data[i,12])==1) print (Y)}
Error in if (grep(data[i, 4], data[i, 12]) == 1) print(Y) :
argument is of length zero
---
here I tested the grep command first and it looks ok. However, when I put it in
for loop, error message came:
argument is of length zero
Could you please help me figure out what happened here?
Thanks a lot for your help.
From: Jeff Newmiller jdnew...@dcn.davis.ca.us
ect.org
Sent: Friday, September 13, 2013 10:36 PM
Subject: Re: [R] problem with grep under loop
Please read the Posting Guide before you post again, and study how to make a
reproducible example of your problem [1], and change the settings on your mail
program to send plain text. I, for one, am not psychic, so need things spelled
out clearly.
[1]
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
---
Jeff Newmiller The . . Go Live...
DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
[[elided Yahoo spam]]
I then first test my data:
dim(data)
[1] 52086 13
if(grep(data[3,4],data[3,12])==1) print(Y)
[1] Y
for(i in 1:52086){if(grep(data[i,4],data[i,12])==1) print (Y)}
Error in if (grep(data[i, 4], data[i, 12]) == 1) print(Y) :
argument is of length zero
What is this new error message? argument is of length zero
Here is my data format:
head(data)
V1 V2 V3 V4 V5 V6
V7 V8
1 ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM
FPKM_conf_lo
2 - - u C.3 C.3.1 100 1.00
0.00
3 - - u C.2 C.2.1 100 1.00
0.00
4 - - u C.4 C.4.1 100 1.00
0.00
5 - - u C.1 C.1.1 100 1.00
0.00
6 - - u C.5 C.5.1 100 1.00
0.00
V9 V10 V11 V12 V13
1 FPKM_conf_hi cov len major_iso_id ref_match_len
2 0.00 0.056682 96 C.3.1 -
3 0.00 0.058453 99 C.2.1 -
4 0.00 0.059634 101 C.4.1 -
5 0.00 0.059634 101 C.2.1 -
6 0.00 0.059634 101 C.5.1 -
From: Jeff Newmiller jdnew...@dcn.davis.ca.us
r-help@r-project.org r-help@r-project.org
Sent: Friday, September 13, 2013 9:21 PM
Subject: Re: [R] problem with grep under loop
This is because you are not printing it (with the print or cat
functions). Keep in mind that the visible result you get from calling a
function or evaluating a variable interactively comes from the
interactive R command line, not from R itself. Once you put such an
expression inside a function (such as the for function) it is no
longer directly being invoked by the command interpreter.
You might want to read [1] and [2] (which says don't post using HTML).
[1]
Re: [R] still about biplot for principal componens analysis
Hi, Jim, Thank you very much for your email. Could you please explain more about the modification about how to adding this pch=1,cex=0.2 to the following command line? biplot(pca2,xlabs=rep(.,19000)) The R document seems to only take text input, whereas pch=1,cex=0.2 are actually graphic parameters... Also the question about points on the biplot are not exactly the same as the predicted values I asked in my previous post, I meant that when I checked the coordinates on the biplot, they are not matching to the pc1 and pc2 values in the predicted output I got from the following command predict(pca2, originalData, ...) Capricy From: Jim Lemon j...@bitwrit.com.au Cc: r-help@r-project.org r-help@r-project.org Sent: Wednesday, May 1, 2013 5:33 AM Subject: Re: [R] still about biplot for principal componens analysis On 05/01/2013 02:46 AM, capricy gao wrote: I noticed that the points on the biplot are not exactly the same as the predicted values. Could any body give me a hint about why? Hi capricy, If you mean the points that would result from the suggestion I sent yesterday, it is probably because using the period (.) character places the dots a bit lower than the actual values. Try using: pch=1,cex=0.2 Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] biplot for principal componens analysis
very helpful!! Thanks a lot. From: Jim Lemon j...@bitwrit.com.au Cc: r-help@r-project.org r-help@r-project.org Sent: Monday, April 29, 2013 6:53 PM Subject: Re: [R] biplot for principal componens analysis On 04/30/2013 08:24 AM, capricy gao wrote: I did a PCA for my data which has a dimension of 19000X4 using princomp pca2=princomp((data), cor=F) and obtained a biplot with 19000 labels which were very busy. How can I just show 19000 spot w/o labels? biplot(pca2) Hi capricy, I suppose you could try: biplot(pca2,xlabs=rep(.,19000)) Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] still about biplot for principal componens analysis
I noticed that the points on the biplot are not exactly the same as the predicted values. Could any body give me a hint about why? Thanks. To: Jim Lemon j...@bitwrit.com.au Cc: r-help@r-project.org r-help@r-project.org Sent: Tuesday, April 30, 2013 9:51 AM Subject: Re: [R] biplot for principal componens analysis very helpful!! Thanks a lot. From: Jim Lemon j...@bitwrit.com.au Cc: r-help@r-project.org r-help@r-project.org Sent: Monday, April 29, 2013 6:53 PM Subject: Re: [R] biplot for principal componens analysis On 04/30/2013 08:24 AM, capricy gao wrote: I did a PCA for my data which has a dimension of 19000X4 using princomp pca2=princomp((data), cor=F) and obtained a biplot with 19000 labels which were very busy. How can I just show 19000 spot w/o labels? biplot(pca2) Hi capricy, I suppose you could try: biplot(pca2,xlabs=rep(.,19000)) Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] still about biplot for principal componens analysis
Looks like my post might get some problems, so I re-wrote my question plus some new one... I noticed that the points on the biplot are not exactly the same as the predicted values. Another relevant question: should I expect that all the vector points have the same length if chose parameters of cor=T , for example, pca2=princomp((data), cor=T)? Could any body give me a hint about any of these questions? Thanks. To: Jim Lemon j...@bitwrit.com.au Cc: r-help@r-project.org r-help@r-project.org Sent: Tuesday, April 30, 2013 9:51 AM Subject: Re: [R] biplot for principal componens analysis very helpful!! Thanks a lot. From: Jim Lemon j...@bitwrit.com.au Cc: r-help@r-project.org r-help@r-project.org Sent: Monday, April 29, 2013 6:53 PM Subject: Re: [R] biplot for principal componens analysis On 04/30/2013 08:24 AM, capricy gao wrote: I did a PCA for my data which has a dimension of 19000X4 using princomp pca2=princomp((data), cor=F) and obtained a biplot with 19000 labels which were very busy. How can I just show 19000 spot w/o labels? biplot(pca2) Hi capricy, I suppose you could try: biplot(pca2,xlabs=rep(.,19000)) Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] biplot for principal componens analysis
I did a PCA for my data which has a dimension of 19000X4 using princomp pca2=princomp((data), cor=F) and obtained a biplot with 19000 labels which were very busy. How can I just show 19000 spot w/o labels? biplot(pca2) Thanks a lot:)) -data A1 A2 L1 L2 E_6 0.23 4.05 13.35 11.86 E_00011 118.74 177.87 144.20 136.05 E_00062 8.50 0.60 73.11 45.81 E_00070 1.31 4.92 0.98 1.23 E_00071 97.41 39.90 31.15 150.77 E_00104 0.00 0.43 18.93 31.28 . . . . . . . . . E_18586 0.00 0.0 0.00 0.95 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot in log scale in both x-axis and y-axis
I am trying to plot(x,y, log=y), which gives me log scale on y axis only. I wonder if there is way so that I can plot log scale on both of x and y axis. Thanks a lot:) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot in log scale in both x-axis and y-axis
Thanks a lot. From: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Thursday, April 4, 2013 3:41 PM Subject: Re: [R] plot in log scale in both x-axis and y-axis I am trying to plot(x,y, log=y), which gives me log scale on y axis only. I wonder if there is way so that I can plot log scale on both of x and y axis. plot(x, y, log = 'xy') Cheers, MW Thanks a lot:) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] looking for help with clustering analysis
My data have good correlations with spearman method and bad correlations with pearson method. If I want to do cluster analysis to reflect the sprearman correlation, what method should I use to calculate the distance matrix? Thanks. Xin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help on dendrogram reorder
I plot a dendrogram using the following code: hc - hclust(dist(USArrests[1:10,]), ave) unlist(as.dendrogram(hc)) [1] 7 1 8 4 6 10 9 2 3 5 how can I easily flip some leaves so that the unlist results are: [1] 7 1 8 4 6 10 9 5 3 2 Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Need help to plot clara results [clustering]
I am going to use clara for gene expression analysis, so tried to play around with the examples from R document: http://127.0.0.1:10699/library/cluster/html/clara.html Everything looked fine until I tried to plot the results: it says: waiting to confirm page change... I waited for more than 10 min and NO plot came out... Should I wait longer? Anything wrong like this? Thanks for any input:) And the code and results: = x - rbind(cbind(rnorm(200,0,8), rnorm(200,0,8)), + cbind(rnorm(300,50,8), rnorm(300,50,8))) clarax - clara(x, 2, samples=50) clarax Call: clara(x = x, k = 2, samples = 50) Medoids: [,1] [,2] [1,] -0.9695444 0.3985362 [2,] 49.4829294 49.9229633 Objective function: 9.786942 Clustering vector: int [1:500] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ... Cluster sizes: 200 300 Best sample: [1] 2 20 21 89 91 104 106 107 129 151 163 188 189 193 217 222 231 235 244 [20] 265 266 288 304 305 313 323 324 339 352 371 387 406 407 412 423 436 441 443 [39] 448 459 461 462 490 494 Available components: [1] sample medoids i.med clustering objective [6] clusinfo diss call silinfo data clarax$clusinfo size max_diss av_diss isolation [1,] 200 24.39542 9.871896 0.3450682 [2,] 300 27.28630 9.730307 0.3859591 all.equal(clarax[-8], + clara(x, 2, samples=50, pamLike = TRUE)[-8]) [1] TRUE plot(clarax) Waiting to confirm page change... [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to subsetting data based on factor levels
Thanks a lot! Cc: R help r-help@r-project.org Sent: Tuesday, March 19, 2013 8:39 PM Subject: Re: [R] How to subsetting data based on factor levels levels(group) #[1] A C levels(group)==A #[1] TRUE FALSE a[,group==A] # A AB #[1,] 1 6 #[2,] 2 7 #[3,] 3 8 #[4,] 4 9 #[5,] 5 10 a[,group==C] # C CD #[1,] 11 16 #[2,] 12 17 #[3,] 13 18 #[4,] 14 19 #[5,] 15 20 a[,match(group,levels(group))==1] # A AB #[1,] 1 6 #[2,] 2 7 #[3,] 3 8 #[4,] 4 9 #[5,] 5 10 A.K. - Original Message - To: r-help r-help@r-project.org Cc: Sent: Tuesday, March 19, 2013 9:19 PM Subject: [R] How to subsetting data based on factor levels Here are the code and results a=matrix(1:20,5) a [,1] [,2] [,3] [,4] [1,] 1 6 11 16 [2,] 2 7 12 17 [3,] 3 8 13 18 [4,] 4 9 14 19 [5,] 5 10 15 20 colnames(a)=c(A,AB,C,CD) a A AB C CD [1,] 1 6 11 16 [2,] 2 7 12 17 [3,] 3 8 13 18 [4,] 4 9 14 19 [5,] 5 10 15 20 group=factor(substring(colnames(a),1,1)) group [1] A A C C Levels: A C a[,levels(group)==A] A C [1,] 1 11 [2,] 2 12 [3,] 3 13 [4,] 4 14 [5,] 5 15 a[,levels(group)==C] AB CD [1,] 6 16 [2,] 7 17 [3,] 8 18 [4,] 9 19 [5,] 10 20 == But, I was expect that: a[,levels(group)==A] A AB [1,] 1 6 [2,] 2 7 [3,] 3 8 [4,] 4 9 [5,] 5 10 [[elided Yahoo spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to subsetting data based on factor levels
Here are the code and results a=matrix(1:20,5) a [,1] [,2] [,3] [,4] [1,] 1 6 11 16 [2,] 2 7 12 17 [3,] 3 8 13 18 [4,] 4 9 14 19 [5,] 5 10 15 20 colnames(a)=c(A,AB,C,CD) a A AB C CD [1,] 1 6 11 16 [2,] 2 7 12 17 [3,] 3 8 13 18 [4,] 4 9 14 19 [5,] 5 10 15 20 group=factor(substring(colnames(a),1,1)) group [1] A A C C Levels: A C a[,levels(group)==A] A C [1,] 1 11 [2,] 2 12 [3,] 3 13 [4,] 4 14 [5,] 5 15 a[,levels(group)==C] AB CD [1,] 6 16 [2,] 7 17 [3,] 8 18 [4,] 9 19 [5,] 10 20 == But, I was expect that: a[,levels(group)==A] A AB [1,] 1 6 [2,] 2 7 [3,] 3 8 [4,] 4 9 [5,] 5 10 Could anybody explain why? Thanks a lot!! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] easy way to install new R version??
Some packages have to be installed on new R version, 2.15.3 but I have 2.15.2 If I don't want to go through all download, and uninstall and install procedures, is there any simple R command that could handle this? Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
