[R] Z score in gplots
Hi, Can anyone tell me how to set Z-score according to my own requirement as the below code is taking as per the file entries. Any help would be appreciable. library(gplots) x=read.table(final.txt, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c(green,white,red))(256), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist, hclustfun = hclust, dendrogram = c(row), scale = c(column), na.rm=TRUE, trace=none, sepwidth=c(0.05,0.05), margins = c(01, 55), xlab = , ylab = , labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c(none), ) Thank you in advance KS [[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] gplot heatmap
Hi, I am drawing a heat map using gplots of R package. The file (new4) is having values 0 and 1 only. library(gplots) library(marray) x=read.table(new4, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c(black,red))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c(row), scale = c(row), na.rm=TRUE, trace=none, sepwidth=c(0.05,0.05), margins = c(25, 20), #xlab = ylab = labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c(none) ) I am giving two color only i.e red and black but when I am try to make the plot it again show in gradients. Therefore, I just want to plot a heat map with two color scheme. Thanks in advance Thank you Khushwant [[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] venn diagramm
Dear Patrick, Thanks for your reply, I know its hectic to c such graphs, as they are difficult to interpret, but I got this interesting link from R http://www.oga-lab.net/RGM2/func.php?rd_id=gplots:venn, mentioned about venn diagram for 5 subsets. ## Example using a list of item names belonging to the ## specified group. ## ## construct some fake gene names.. oneName - function() paste(sample(LETTERS,5,replace=TRUE),collapse=) geneNames - replicate(1000, oneName()) ## GroupA - sample(geneNames, 400, replace=FALSE) GroupB - sample(geneNames, 750, replace=FALSE) GroupC - sample(geneNames, 250, replace=FALSE) GroupD - sample(geneNames, 300, replace=FALSE) input -list(GroupA,GroupB,GroupC,GroupD) input venn(input) But not sure how to give files, as in this example I think they are giving at terminal, I am not sure this is hard to understand for me. But I will try it with different sides and I hope I will get something of of it. But if you also extract some good plz let me know. I also got a online tool called venny to draw for 4 subsets. Thanks khush On Sat, May 7, 2011 at 10:28 PM, Breheny, Patrick patrick.breh...@uky.eduwrote: I've never actually used it with 5 subsets, but the 'venn' function in the gplots package claims to be able to make a Venn diagram with up to 5 subsets. --Patrick From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of khush [bioinfo.kh...@gmail.com] Sent: Saturday, May 07, 2011 9:54 AM To: r-help@r-project.org Subject: [R] venn diagramm Dear all, I have a set of five datasets with string, for which I need to draw the venn diagram. there are tools available to draw venn diagram online, but limited to three sets. I can also generate venn for three from limma package, but do not know how to proceed with five subsets. Help me in drawing the same any script . Thank you Khush [[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] venn diagramm
Dear all, I have a set of five datasets with string, for which I need to draw the venn diagram. there are tools available to draw venn diagram online, but limited to three sets. I can also generate venn for three from limma package, but do not know how to proceed with five subsets. Help me in drawing the same any script . Thank you Khush [[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] Clustering help in Heat Maps
Dear Experts,
I am using the below script to generate the heat map of gene expression
data. I am using Hierarchical Clustering (hclust) for clustering. Now I want
to compare different clustering parameters such as *K-means* clustering, Model
Based Clustering,
I have two queries:
1. How to incorporate different clustering method in the same code?
2. Is this possible to implement pvclust in the same code and cluster
accordingly?
library(gplots)
#===Cyto=
#x=read.table(Cyto_shoot.txt, header=TRUE)
mat=data.matrix(x)
heatmap.2(mat,
# c('red','green','orange','blue','yellow',
'gray','black','brown','aquamarine3','cyan',
'darkmagenta','darkviolet','green4'))
col=colorRampPalette(c(green,white,red))(256),
#col=greenred(75),
#col = cm.colors(256),
#bgStyle=3D Rectangle,
#bgGradientMode= Diagonal Edge,
Rowv=TRUE,
Colv=FALSE,
distfun = dist,
hclustfun = hclust,
dendrogram = c(row),
scale = c(column),
na.rm=TRUE,
trace=none,
sepwidth=c(0.05,0.05),
margins = c(03, 40),
xlab = , ylab = ,
labRow = NULL,
labCol = NULL,
key=TRUE,
keysize=1,
density.info=c(none),
)
Thanks in advance
Kamal
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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] Drawing Heatmap using gplots
Hi, I am using heatmap.2 of gplots to make heatmaps of my the attached file. I am giving my code for the same .. library(gplots) x=read.table(1.txt, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c(both), scale = c(row), na.rm=TRUE, trace=none, sepwidth=c(0.05,0.05), margins = c(5, 10), xlab = EXPRESSIONS, ylab = GENES, labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c(none), ) I have certain queries regarding the same. 1. why the heat map is totally different from what the sequence of information is? 2. Is there any way to arrange the data based on the expression pattern of the genes or some other way, which make some sense out of data. 3. I have some color issues as the number of genes increases the green and black colors are not as much as prominent as red? Thank you so much for your help in advance. Thank you Khushwant CAF CAS INF INS AP1 AP3 AGM SAP S04 S52 LEF LES ROF ROS GSE SIF SIS At1g01940 107 111 20 27 40 52 27 8 6 24 40 18 67 85 35 56 118 At1g26940 35 27 30 28 15 41 12 73 6 15 21 11 60 35 6 24 77 At1g53720 34 35 16 52 15 27 24 13 3 12 35 6 43 51 1 21 25 At1g53780 2 6 2 11 6 9 7 0 0 0 6 10 5 19 0 0 0 At1g74070 0 16 18 41 18 23 13 9 68 7 41 39 0 6 29 66 53 At2g15790 0 61 0 2 1 1 2 0 0 5 0 0 0 8 0 0 47 At2g16600 703 1157414 299 616 12351208645 25743308473 183 17971156455 735 596 At2g21130 240 154 270 615 78 265 1257769 704 126 16 22 70 1 20 140 208 At2g29960 81 145 23 45 62 37 49 25 52 39 48 27 31 151 0 35 293 At2g36130 248 36 88 46 32 110 86 58 10 6 278 34 252 96 0 190 84 At2g38730 26 8 16 6 4 18 0 0 0 0 0 0 6 1 0 22 0 At2g47320 105 82 87 88 42 91 118 158 84 96 87 132 394 301 30 378 302 At3g01480 0 6 174 48 36 159 52 79 56 101 0 88 8 2 103 207 41 At3g15520 0 0 86 70 30 52 17 19 47 7 70 43 68 0 33 38 45 At3g22920 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 At3g44600 62 166 62 48 24 39 26 14 0 4 56 32 106 155 2 28 18 At3g55920 42 52 27 6 11 28 25 68 82 10 15 33 27 17 1 24 81 At3g56070 234 136 112 136 112 260 128 150 0 24 106 18 322 222 20 70 88 At3g62030 34 109 241 129 181 338 304 595 463 849 810 406 18 94 399 566 1992 At3g63400 138 138 144 60 63 57 60 26 53 32 82 66 143 127 91 87 37 At3g66654 79 45 37 15 16 16 23 17 0 59 88 25 40 65 12 50 23 At4g17070 39 103 4 18 33 19 22 33 15 81 56 28 7 100 32 7 41 At4g32420 71 112 59 125 81 103 108 93 30 11 69 30 17 80 7 24 93 At4g33060 164 106 70 20 23 42 23 9 0 14 39 47 74 92 14 222 252 At4g34870 299016 3272320 421 433 311 434 104 19 153297 6519312 345 316075 At4g34960 101 38 300 1 1 7 2 0 0 0 33 0 172 14 0 118 52 At4g38740 503422721986
[R] Drawing Heatmap using gplots
Hi, I am using heatmap.2 of gplots to make heatmaps of my the file. I am giving my code for the same .. library(gplots) x=read.table(1.txt, header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c(both), scale = c(row), na.rm=TRUE, trace=none, sepwidth=c(0.05,0.05), margins = c(5, 10), xlab = EXPRESSIONS, ylab = GENES, labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c(none), ) my file is like this ... CAF CAS INF INS AP1 AP3 AGM SAP S04 S52 LEF LES ROF ROS GSE SIF SIS At1g01940 107 111 20 27 40 52 27 8 6 24 40 18 67 85 35 56 118 At1g26940 35 27 30 28 15 41 12 73 6 15 21 11 60 35 6 24 77 At1g53720 34 35 16 52 15 27 24 13 3 12 35 6 43 51 1 21 25 At1g53780 2 6 2 11 6 9 7 0 0 0 6 10 5 19 0 0 0 At1g74070 0 16 18 41 18 23 13 9 68 7 41 39 0 6 29 66 53 At2g15790 0 61 0 2 1 1 2 0 0 5 0 0 0 8 0 0 47 At2g16600 703 1157414 299 616 12351208 645 25743308473 183 17971156455 735 596 At2g21130 240 154 270 615 78 265 1257 769 704 126 16 22 70 1 20 140 208 At2g29960 81 145 23 45 62 37 49 25 52 39 48 27 31 151 0 35 293 At2g36130 248 36 88 46 32 110 86 58 10 6 278 34 252 96 0 190 84 At2g38730 26 8 16 6 4 18 0 0 0 0 0 0 6 1 0 22 0 At2g47320 105 82 87 88 42 91 118 158 84 96 87 132 394 301 30 378 302 At3g01480 0 6 174 48 36 159 52 79 56 101 0 88 8 2 103 207 41 At3g15520 0 0 86 70 30 52 17 19 47 7 70 43 68 0 33 38 45 At3g22920 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 At3g44600 62 166 62 48 24 39 26 14 0 4 56 32 106 155 2 28 18 I have certain queries regarding the same. 1. why the heat map is totally different from what the sequence of information is? 2. Is there any way to arrange the data based on the expression pattern of the genes or some other way, which make some sense out of data. 3. I have some color issues as the number of genes increases the green and black colors are not as much as prominent as red? Thank you so much for your help in advance. Thank you Khushwant [[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] Argument lib is missing
Dear all, I have installed R using yum install R-2.9. I am able to use R for general functions but when I installed some library say gplots I am getting the below error. install.packages(gplots) Warning in install.packages(gplots) : argument 'lib' is missing: using '/home/fedora/R/i386-redhat-linux-gnu-library/2.11' Warning: unable to access index for repository http://cran.csdb.cn/src/contrib Warning message: In getDependencies(pkgs, dependencies, available, lib) : package gplots is not available any suggestion will be appreciable. Thank you Khush [[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] R code changes to crap
Hi, I am using vim to edit my files...I do not know what has been pressed by me as my R code get converted to such a crap... %PDF-1.4 %81â81ã81Ï81Ó\r 1 0 obj /CreationDate (D:20100902122215) /ModDate (D:20100902122215) /Title (R Graphics Output) /Producer (R 2.11.1) /Creator (R) how to reconvert it to the my actual code?? as I do not have backup for it..? Thanks in advance Khushwant [[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] Save data as .pdf or .JPG
Hi all , I have following script to plot some data. plot( c(1,1100), c(0,15), type='n', xlab='', ylab='', ylim=c(0.1,25) , las=2) axis (1, at = seq(0,1100,50), las =2) axis (2, at = seq(0,25,1), las =2) lines( c(1,304),c(0,0),col='grey', lwd=3 ) lines( c(1,238),c(1,1),col='grey', lwd=3 ) segments(86, 0,270,col = green, pch=23, cex=9, lty=solid, lwd=14,lend=2) segments(74,1,238,col = green, pch=23, cex=9, lty=solid, lwd=14,lend=2) When I source(script.R), I got the image on interface but I do not want to use screenshot option to save the image? How can save the output to .pdf or .jpg format? Thanks in advance Thank you Khushwant [[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] points marking
Hej Gregory,
Thanks for your reply and sorry for late reply, actually I was busy with
some other stuff but It helped me alot.
Thanks again sir.
Thanks to both of you.
Thank you
Jeet
On Wed, Jun 16, 2010 at 2:27 AM, Greg Snow greg.s...@imail.org wrote:
OK, I did not see the website before, here is some code to replicate the
example shown there (except I dont do 3D effects):
library(TeachingDemos)
plot( c(1,1000), c(1,5), type='n', xlab='', ylab='', yaxt='n',
ylim=c(0.5,5.5) )
tmpfun - function( n, col, txt, cex=.5 ) {
plot.window( c(-1,1), c(-1,1) )
ms.filled.polygon( n=n, fg=col, bg=col, adj=0 )
shadowtext(0,0, txt, cex=cex)
}
lines( c(1,700), c(1,1), col='grey', lwd=3 )
lines( c(100,100,200,200), c(1,1.25,1.25,1) )
lines( c(320,320), c(1,1.25), col='red' )
points( 320, 1.25, pch=18, col='red' )
subplot( tmpfun(400, 'grey15', 'MY'), c(50, 150), c(0.85,1.15) )
subplot( tmpfun(5, 'green', 'DOM'), c(300, 400), c(0.85, 1.15) )
Hope this helps get you started (this could all be wrapped into a single
function if you want, additional proteins can be added at 2, 3,
),
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
*From:* khush [mailto:bioinfo.kh...@gmail.com]
*Sent:* Monday, June 14, 2010 11:21 PM
*To:* Greg Snow
*Cc:* Petr PIKAL
*Subject:* Re: [R] points marking
Dear Gregory ,
Thanks for your kind reply, and consideration towards my query, well have
you check with the link that I sent you the other day (
http://www.expasy.ch/tools/mydomains/), in which you need to set the
protein length first and then the domain data, with various shapes i.e 1-6
and 4 different colors respectively.
In the second part of the example,
50 ,150 , 2,4, MY
300 ,400 , 3,2, DOM
I am drawing all the data with barplots as they are so many so I am using
barplots, and they are of variuos length, as I mentioned in Dom (has all the
protein lengths in it), now I wanted to draw various shapes to my data say
on bar 1 of barplots segments 50-150 has shapes say x and color = red, adn
its name is MY , and this could repeat for other bars of the plot but with
different points .
same like other if I want to plot the segments 300-400 with shapes say y
and color = red and its name should be DOM
I want to make a script which could take the length of the protein and draw
corresponding domains on it. Hope you understand the way I am explaining you
now. Please feel free to ask further if needed.
Thank you
Jeet
On Mon, Jun 14, 2010 at 9:13 PM, Greg Snow greg.s...@imail.org wrote:
I dont think that I would use a barplot as the base, but rather just set
up the graph and add the lines where I wanted them. I still dont
understand what you want your graph to look like, or what question you are
trying to answer with it (part may be a language barrier). If you can give
us a better example of what you are trying to accomplish, or a better
description of what your data is like and what you are trying to get from
the graph, we will have a better chance of being able to help you.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
*From:* khush [mailto:bioinfo.kh...@gmail.com]
*Sent:* Saturday, June 12, 2010 5:38 AM
*To:* Greg Snow
*Cc:* r-help@r-project.org; Petr PIKAL
*Subject:* Re: [R] points marking
Hi,
Well Thanks for letting me know that pch is of no use with segments petr. I
am using lend as it suits to me more as gregory suggested , but I am not
getting imite??? think I try to fix it with some other method also, as I
have to deal more with the symbols in this case, But I want to the know one
thing from you guys that the way I am using the code is good enough to
start, as I am not much familiar with this suff or its dirty way to handle
such task. please let me know.
Thanks gregory and petr.
Thank you
Jeet
On Fri, Jun 11, 2010 at 9:07 PM, Greg Snow greg.s...@imail.org wrote:
Those graphs look like chromosome maps, if so, you may want to look into
the bioconductor project, they may have some prewritten functions to do
this. If not, the lend argument (see ?par) may be something to look at. If
you really want points and segments you will need to plot the points with
the points function and the segments separately. Segments can take vectors,
so you dont need to separate things into multiple calls.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
*From:* khush [mailto:bioinfo.kh...@gmail.com]
*Sent:* Friday, June 11, 2010 12:00 AM
*To:* Greg Snow
*Cc:* r-help@r-project.org
*Subject:* Re: [R] points marking
Dear Gregory ,
Thnaks for your reply and help. I am explaining you my problems
Re: [R] points marking
Hi, Well Thanks for letting me know that pch is of no use with segments petr. I am using lend as it suits to me more as gregory suggested , but I am not getting imite??? think I try to fix it with some other method also, as I have to deal more with the symbols in this case, But I want to the know one thing from you guys that the way I am using the code is good enough to start, as I am not much familiar with this suff or its dirty way to handle such task. please let me know. Thanks gregory and petr. Thank you Jeet On Fri, Jun 11, 2010 at 9:07 PM, Greg Snow greg.s...@imail.org wrote: Those graphs look like chromosome maps, if so, you may want to look into the bioconductor project, they may have some prewritten functions to do this. If not, the lend argument (see ?par) may be something to look at. If you really want points and segments you will need to plot the points with the points function and the segments separately. Segments can take vectors, so you dont need to separate things into multiple calls. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 *From:* khush [mailto:bioinfo.kh...@gmail.com] *Sent:* Friday, June 11, 2010 12:00 AM *To:* Greg Snow *Cc:* r-help@r-project.org *Subject:* Re: [R] points marking Dear Gregory , Thnaks for your reply and help. I am explaining you my problems again, below is my script for the same . Dom -c (195,568,559) fkbp - barplot (Dom, col=black, xlab=, border = NA, space = 7, xlim=c(0,650), ylim =c(0, 87), las = 2, horiz = TRUE) axis (1, at = seq(0,600,10), las =2) 1. ==Segments 1= segments(164,7.8,192,7.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(45,15.8,138,15.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(160,15.8,255,15.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(277,15.8,378,15.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(51,23.8,145,23.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(167,23.8,262,23.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(284,23.8,381,23.8, col = green, pch=23, cex=9, lty=solid, lwd=20) 2. ==Segments 2 == segments(399,15.8,432,15.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(448,15.8,475,15.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(486,15.8,515,15.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(401,23.8,434,23.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(450,23.8,475,23.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(486,23.8,517,23.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) I solved one part of my query i.e to mark points from one positions to other is ok and I found that its working fine but I have another issue now, as I am using using two segments data 1 and 2 , although I want to draw different shapes for segmants 2 as I am giving pch=21, but I it seems to give a solid line for both. I want to draw different shapes for every chunk of segments i.e is the whole point. I want to make script which can generate such figures, below is link to one of the tool. http://www.expasy.ch/tools/mydomains/ Thank you Jeet On Thu, Jun 10, 2010 at 11:10 PM, Greg Snow greg.s...@imail.org wrote: Your question is not really clear, do either of these examples do what you want? with(anscombe, plot(x1, y2, ylim=range(y2,y3)) ) with(anscombe, points(x1, y3, col='blue', pch=2) ) with(anscombe, segments(x1, y2, x1, y3, col=ifelse( y2y3, 'green','red') ) ) with(anscombe, plot(x1, y2, ylim=range(y2,y3), type='n') ) with(anscombe[order(anscombe$x1),], polygon( c( x1,rev(x1) ), c(y2, rev(y3)), col='grey' ) ) -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of khush Sent: Thursday, June 10, 2010 7:48 AM To: r-help@r-project.org Subject: [R] points marking Hi, How to mark points on x axis of a graph keeping x axis as constant and changing y from y1 to y2 respectively. I want to highlight the area from y1 to y2. Any suggestions Thank you Jeet [[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
Re: [R] points marking
Dear Gregory , Thnaks for your reply and help. I am explaining you my problems again, below is my script for the same . Dom -c (195,568,559) fkbp - barplot (Dom, col=black, xlab=, border = NA, space = 7, xlim=c(0,650), ylim =c(0, 87), las = 2, horiz = TRUE) axis (1, at = seq(0,600,10), las =2) 1. ==Segments 1= segments(164,7.8,192,7.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(45,15.8,138,15.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(160,15.8,255,15.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(277,15.8,378,15.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(51,23.8,145,23.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(167,23.8,262,23.8, col = green, pch=23, cex=9, lty=solid, lwd=20) segments(284,23.8,381,23.8, col = green, pch=23, cex=9, lty=solid, lwd=20) 2. ==Segments 2 == segments(399,15.8,432,15.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(448,15.8,475,15.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(486,15.8,515,15.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(401,23.8,434,23.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(450,23.8,475,23.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) segments(486,23.8,517,23.8, col = blue, pch=21, cex=9, lty=solid, lwd=20) I solved one part of my query i.e to mark points from one positions to other is ok and I found that its working fine but I have another issue now, as I am using using two segments data 1 and 2 , although I want to draw different shapes for segmants 2 as I am giving pch=21, but I it seems to give a solid line for both. I want to draw different shapes for every chunk of segments i.e is the whole point. I want to make script which can generate such figures, below is link to one of the tool. http://www.expasy.ch/tools/mydomains/ Thank you Jeet On Thu, Jun 10, 2010 at 11:10 PM, Greg Snow greg.s...@imail.org wrote: Your question is not really clear, do either of these examples do what you want? with(anscombe, plot(x1, y2, ylim=range(y2,y3)) ) with(anscombe, points(x1, y3, col='blue', pch=2) ) with(anscombe, segments(x1, y2, x1, y3, col=ifelse( y2y3, 'green','red') ) ) with(anscombe, plot(x1, y2, ylim=range(y2,y3), type='n') ) with(anscombe[order(anscombe$x1),], polygon( c( x1,rev(x1) ), c(y2, rev(y3)), col='grey' ) ) -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of khush Sent: Thursday, June 10, 2010 7:48 AM To: r-help@r-project.org Subject: [R] points marking Hi, How to mark points on x axis of a graph keeping x axis as constant and changing y from y1 to y2 respectively. I want to highlight the area from y1 to y2. Any suggestions Thank you Jeet [[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] points marking
Hi, How to mark points on x axis of a graph keeping x axis as constant and changing y from y1 to y2 respectively. I want to highlight the area from y1 to y2. Any suggestions Thank you Jeet [[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] rgl installation failure
Hello, I am trying to install rgl package under R and getting some errors which is below. install.packages(rgl) Warning in install.packages(rgl) : argument 'lib' is missing: using '/usr/lib/R/library' trying URL 'http://cran.csie.ntu.edu.tw/src/contrib/rgl_0.91.tar.gz' Content type 'application/x-gzip' length 1677498 bytes (1.6 Mb) opened URL == downloaded 1.6 Mb * installing *source* package rgl ... checking for gcc... gcc -m32 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -m32 -std=gnu99 accepts -g... yes checking for gcc -m32 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E checking for gcc... (cached) gcc -m32 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc -m32 -std=gnu99 accepts -g... (cached) yes checking for gcc -m32 -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... no checking libpng... checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking png.h usability... no checking png.h presence... no checking for png.h... no checking for png_read_update_info in -lpng... no configure: libpng header and lib found configure: using libpng dynamic linkage checking for X... libraries , headers checking GL/gl.h usability... yes checking GL/gl.h presence... yes checking for GL/gl.h... yes checking GL/glu.h usability... yes checking GL/glu.h presence... yes checking for GL/glu.h... yes checking for glEnd in -lGL... yes checking for gluProject in -lGLU... yes checking for freetype-config... yes configure: using Freetype and FTGL configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -m32 -I/usr/include/R -DHAVE_PNG_H -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c BBoxDeco.cpp -o BBoxDeco.o g++ -m32 -I/usr/include/R -DHAVE_PNG_H -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c Background.cpp -o Background.o g++ -m32 -I/usr/include/R -DHAVE_PNG_H -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c Color.cpp -o Color.o g++ -m32 -I/usr/include/R -DHAVE_PNG_H -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c Disposable.cpp -o Disposable.o g++ -m32 -I/usr/include/R -DHAVE_PNG_H -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c Light.cpp -o Light.o g++ -m32 -I/usr/include/R -DHAVE_PNG_H -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom
Re: [R] rgl installation failure
Hi, Thanks Berwin for your suggestions , sorry to mention but it was fedora 12 OS that I am using. Actually I was missing libraries png which I installed using yum and it work good now. Earlier png.h was missing in /usr/includes/ but its is showing . Thanks alot for your kind help. Cheers Thank you Jeet On Sat, Jun 5, 2010 at 1:07 PM, Berwin A Turlach ber...@maths.uwa.edu.auwrote: G'day, On Sat, 5 Jun 2010 12:51:08 +0530 khush bioinfo.kh...@gmail.com wrote: I am trying to install rgl package under R and getting some errors which is below. install.packages(rgl) Warning in install.packages(rgl) : argument 'lib' is missing: using '/usr/lib/R/library' trying URL 'http://cran.csie.ntu.edu.tw/src/contrib/rgl_0.91.tar.gz' Content type 'application/x-gzip' length 1677498 bytes (1.6 Mb) opened URL == downloaded 1.6 Mb * installing *source* package _rgl_ ... checking for gcc... gcc -m32 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -m32 -std=gnu99 accepts -g... yes checking for gcc -m32 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E checking for gcc... (cached) gcc -m32 -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc -m32 -std=gnu99 accepts -g... (cached) yes checking for gcc -m32 -std=gnu99 option to accept ISO C89... (cached) none needed checking for libpng-config... no checking libpng... checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking png.h usability... no checking png.h presence... no checking for png.h... no checking for png_read_update_info in -lpng... no You should heed indications as the above, i.e. that items checked for are not found. [...] In file included from pixmap.cpp:14: pngpixmap.h:3:17: error: png.h: No such file or directory And this compiler error seems to be directly linked to the issues identified by configure; and all further error come from the fact that png.h cannot be found. You seem to be using some flavour of Unix, presumably GNU/Linux; but from your posting it is impossible to say which one. On a Debian based system (e.g. Kubuntu 9.10 which I am using), I would issue the command (assuming that apt-file is installed and initialised): ber...@bossiaea:~$ apt-file find include/png.h libpng12-dev: /usr/include/png.h and then check whether the libpng12-dev package is installed. If not, I would install it and retry. Perhaps that would be all that is needed to compile rgl, but there might be other packages missing. If you have a system based on RedHat and Suse, you will have to figure out how to use the package management tools on those systems to find out which packages have to be installed additionally so that you are able to compile rgl. HTH. Cheers, Berwin == Full address Berwin A Turlach Tel.: +61 (8) 6488 3338 (secr) School of Maths and Stats (M019)+61 (8) 6488 3383 (self) The University of Western Australia FAX : +61 (8) 6488 1028 35 Stirling Highway Crawley WA 6009e-mail: ber...@maths.uwa.edu.au Australia http://www.maths.uwa.edu.au/~berwinhttp://www.maths.uwa.edu.au/%7Eberwin [[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] Shapes in barplots
Hi,
I am making barplots . I am using the default shape of barplots with a pipe
but I wants to build bars in various 3d shapes. I have install rgl using
install.packages('rgl') for this purpose, but when I am doing library(rgl),
it shows
Error in library(rgl) : there is no package called 'rgl'
What are the other ways to build such plots of variuos shapes.
Is that *TeachingDemos *replace it..I am not sure how to use it for such
task.
Thanks in advance
Jeet
[[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] Shapes in barplots
Dear Gregory,
Well Thanks for your suggestions. I am no more using TeachingDemos for the
same. I am installing rgl for the same, but one thing I want to ask like I
need to make round ended bars instead of normal one I have to look into rgl
for the same, but is there any option which you think suitable for me in
barplots. Whats your suggestions.
Thank you
Jeet
On Fri, Jun 4, 2010 at 11:09 PM, Greg Snow greg.s...@imail.org wrote:
The TeachingDemos package does not in any way replace the rgl package.
They serve very different purposes (the TeachingDemos package does use rgl
for a couple of functions).
I would be very surprised if there was anything in the TeachingDemos
package that would be of help in creating barplots with 3d effects. 3d
effects distort the information in graphs without adding anything to their
interpretation.
If you want to display information, then use the appropriate graph without
the extra chartjunk. If you want something to catch the reader's attention,
use a picture of a kitten.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of khush
Sent: Friday, June 04, 2010 1:45 AM
To: r-help@r-project.org
Subject: [R] Shapes in barplots
Hi,
I am making barplots . I am using the default shape of barplots with a
pipe
but I wants to build bars in various 3d shapes. I have install rgl
using
install.packages('rgl') for this purpose, but when I am doing
library(rgl),
it shows
Error in library(rgl) : there is no package called 'rgl'
What are the other ways to build such plots of variuos shapes.
Is that *TeachingDemos *replace it..I am not sure how to use it for
such
task.
Thanks in advance
Jeet
[[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] Help barplots
Hi all, I want to draw a arrow (small) of any length along with OsCYP right side i.e parrallel and antiparallel arrows both text(os[1], 10.2, pos = 4, OsCYP, font=1, cex = 1, col = red) and how can I connect two points with dotted line lets say bp[1 ]10.2 bp[3], 15.2 how to make a dotted line using R, is it possible Thank you in advance Jeet On Tue, Jun 1, 2010 at 4:31 PM, khush bioinfo.kh...@gmail.comwrote: Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, chromosome - c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) barplot (chromosome, col=purple, xlab=Oryza sativa Chromosomes, border = NA, space = 5, ylim = c(0,45)) I wanted to mark the position say on chromosome 1 (40.2) I need to mark 10.2 and on other also. I also want to set the scale of y axis from 0,5,10,15,20,25,30,35,40,45 i.e gap of 5 instead of 10. please help me to solve my querygurus. Thank you Jeet [[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 barplots
Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, chromosome - c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) barplot (chromosome, col=purple, xlab=Oryza sativa Chromosomes, border = NA, space = 5, ylim = c(0,45)) I wanted to mark the position say on chromosome 1 (40.2) I need to mark 10.2 and on other also. I also want to set the scale of y axis from 0,5,10,15,20,25,30,35,40,45 i.e gap of 5 instead of 10. please help me to solve my querygurus. Thank you Jeet [[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] Help barplots
Dear All, Thank you very much for your kind help and support I got it. Jeet On Tue, Jun 1, 2010 at 5:32 PM, Jim Lemon j...@bitwrit.com.au wrote: On 06/01/2010 09:01 PM, khush wrote: Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, chromosome- c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) barplot (chromosome, col=purple, xlab=Oryza sativa Chromosomes, border = NA, space = 5, ylim = c(0,45)) I wanted to mark the position say on chromosome 1 (40.2) I need to mark 10.2 and on other also. I also want to set the scale of y axis from 0,5,10,15,20,25,30,35,40,45 i.e gap of 5 instead of 10. please help me to solve my querygurus. Hi Jeet, I think you want the x positions of the bars. Get them like this: xpos-barplot (chromosome, col=purple, xlab=Oryza sativa Chromosomes, border = NA, space = 5, ylim = c(0,45)) Then you can place the extra labels using the values in xpos. For the custom y axis, add the argument yaxt=n to your plot command and then add the axis later. I suspect you will have to use something like the staxlab function in the plotrix package to get all those labels to display. 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.
