Re: [R] find points on a graph
May i please update my question, and I understand now something that i did not yesterday. In this example: table - structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c(gene1, gene2, gene3, gene4, gene5), c(codon1, codon2, codon3))) Library(ca) list -scan(test_list, what=list(gene=)) ### where test_list is a file containing the words gene4, gene5 plot(ca(table, suprow=c(4, 5))) *Question 1: is it possible to change:* plot(ca(table, suprow=c(4, 5))) to either: plot(ca(table, suprow=c(0-100)) ## e.g. a range of numbers (i have about 100 rows that i need to highlight, so i'd rather not do manually) or: plot(ca(table, suprow=c(test_list))) ### where i've given it a file with list of nodes, and R can find the rows that these nodes are on and highlight these. And then my second question is the same as previous regarding the plot output, is it possible to shade rather than have open circles. Many thanks. -- View this message in context: http://r.789695.n4.nabble.com/find-points-on-a-graph-tp4452746p4459001.html Sent from the R help mailing list archive at Nabble.com. __ 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] find points on a graph
Thank you. I really appreciate the help. May i ask two questions. In the example below: table - structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c(gene1, gene2, gene3, gene4, gene5), c(codon1, codon2, codon3))) Library(ca) plot(ca(table, suprow=c(4, 5))) i get an output plot like this: http://r.789695.n4.nabble.com/file/n4456264/Screen_shot_2012-03-08_at_12.16.41.png is it possible to add in code somewhere so that the nodes of interest are not open circles, but are encompassed by a shading on them, similar to this: http://r.789695.n4.nabble.com/file/n4456264/Screen_shot_2012-03-08_at_12.18.34.png And my second question, in this line of the code here: plot(ca(table, suprow=c(4, 5))) is it possible to edit suprow=c(4, 5) to say suprow=c(the genes that are in a certain file), i.e rather than manually type each gene in, get the code to read in a file? When i try move gene 4 and gene 5 to a seperate file, and try to read it in, i get: plot - ca(table,suprow=c(file)) Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic Many thanks for your time. -- View this message in context: http://r.789695.n4.nabble.com/find-points-on-a-graph-tp4452746p4456264.html Sent from the R help mailing list archive at Nabble.com. __ 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] find points on a graph
Hey guys, Can anyone help? I did a correspondance analysis and made a plot. I also have a specific list of nodes that i want to find in my plot and want to either color the nodes that appear in my list differently, or put some kind of border around that group of nodes... Would anyone know how to do this? Also, would this post be more relevant here or in the bioconductor forum? -- View this message in context: http://r.789695.n4.nabble.com/find-points-on-a-graph-tp4452746p4452746.html Sent from the R help mailing list archive at Nabble.com. __ 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] find points on a graph
Le mercredi 07 mars 2012 à 01:40 -0800, aoife a écrit : Hey guys, Can anyone help? I did a correspondance analysis and made a plot. I also have a specific list of nodes that i want to find in my plot and want to either color the nodes that appear in my list differently, or put some kind of border around that group of nodes... Would anyone know how to do this? Not if you don't tell us what package and function you used for this CA. Can you provide a small reproducible example? Regards __ 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] find points on a graph
Many thanks for your reply. Yes absolutely. So this is a small example: library(ca) table - read.table(test, header=TRUE) table codon1 codon2 codon3 gene14.0 7 11 gene27.0222 8 gene30.2 3 8 ca_analysis - ca(table) plot - plot(ca_analysis) and then i took a screen shot of the plot i can see. http://r.789695.n4.nabble.com/file/n4453046/Screen_shot_2012-03-07_at_12.00.44.png so now for example i have a seperate file with 2 gene names: gene2 gene3 and i want to find these two genes/nodes on the graph, and either highlight them a different color, or draw a border/shade them in some way. basically highlight them in any way? is this any more helpful to explain what i mean? Aoife -- View this message in context: http://r.789695.n4.nabble.com/find-points-on-a-graph-tp4452746p4453046.html Sent from the R help mailing list archive at Nabble.com. __ 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] find points on a graph
You did not provide reproducible data since you didn't give us the test file or any values for gene4 and gene5. You should read the posting guideline (particularly the use of dput) and the documentation for package ca. I'm assuming that you want to plot supplementary rows (as described in the ca documentation). Using your values, making some up for gene4 and gene5, and combining them with the original data, you want the following: table - structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c(gene1, gene2, gene3, gene4, gene5), c(codon1, codon2, codon3))) Library(ca) plot(ca(table, suprow=c(4, 5))) This uses the first 3 rows for the correspondence analysis and then plots rows 4 and 5 in that space using an open circle. -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of aoife Sent: Wednesday, March 07, 2012 6:03 AM To: r-help@r-project.org Subject: Re: [R] find points on a graph Many thanks for your reply. Yes absolutely. So this is a small example: library(ca) table - read.table(test, header=TRUE) table codon1 codon2 codon3 gene14.0 7 11 gene27.0222 8 gene30.2 3 8 ca_analysis - ca(table) plot - plot(ca_analysis) and then i took a screen shot of the plot i can see. http://r.789695.n4.nabble.com/file/n4453046/Screen_shot_2012-03- 07_at_12.00.44.png so now for example i have a seperate file with 2 gene names: gene2 gene3 and i want to find these two genes/nodes on the graph, and either highlight them a different color, or draw a border/shade them in some way. basically highlight them in any way? is this any more helpful to explain what i mean? Aoife -- View this message in context: http://r.789695.n4.nabble.com/find- points-on-a-graph-tp4452746p4453046.html Sent from the R help mailing list archive at Nabble.com. __ 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@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.
