similar to: can't install plotrix

Hello, I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the channel of interest eg. Cy5 or Cy3 across the set of experiments). I might have missed a straight forward

Hi all, I have a large table mapping thousands of COGs(groups of genes) to pathways. # Ex COG0001 patha pathb pathc COG0002 pathd pathe COG0003 pathe pathf pathg pathh ## I would like to combine this information into a big list such as below COG2PATHWAY<- list (COG0001 = c ("patha ","pathb ","pathc

Hi all, I have 6 datasets(dataframes Assem_ContigsLen7 through all_ContigsLen12) containing 3 columns (contig_id, contig_length, read_count). Each dataset is composed of 3 types of contigs (assemblies of genomic fragments), 1- all Bacterial fragments, 2 - all Viral fragments, 3 - mixed fragments. I identified the type of contig through a merge with another table with just contig_id and

Hi all, I have some data as follows. Cat1 Cat2 Cat3 COG Counts A B C COG1 10 B D COG2 20 C COG3 30 D COG4 40 I would like to sum all the counts for each category: A B C D 10 30 40 60 >CAT2COG<-

Dear all, I want to use string split to parse column names, however, I am having some errors that I don't understand. I see a problem when I try to rbind the output from strsplit. please let me know if I'm missing something obvious, thanks, alison here are my commands: >strsplit<-strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\\.") >

Hello, I am using RmySQL and would like to iterate through a few queries. I would like to use sprintf but I think I'm having problems mixing and matching the sprintf syntax and the SQL regex. I have checked my sqlcmd and it works when I wan to match %MG1% but how do I iterate for i 1-72? Escape characters,? thanks in advance i<-1 sqlcmd_ScaffLen<-sprintf('SELECT scaffold.length

Here are the error messages: > install.packages('plotrix') Warning in install.packages("plotrix") : argument 'lib' is missing: using '/Users/dbae/Library/R/library' --- Please select a CRAN mirror for use in this session --- Error in .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, : unable to create temporary directory

I am trying to draw a polar plot, which is easy enough to do in the plotrix package through the polar.plot function. However I would like to change the origin of the length vector. For instance all my length values are between 75 and 85, so instead of having the origin as 0 (the default) I'd like it to be, say, 50. Is there any way do to this in the polar.plot function, or if not is there an

Dear All, I am using the plotrix library to plot some matrices. I have a problem: some of my data are outliers, hence using a linear color scale does not work very well (you would see too many cells having a similar, indistinguishable color). See the code snipped at the end of the email. Plotting the logarithm of the data gets the job done, but my problem is that I would like to write in every

Dear All, Please see the code snippet at the end of the email. I am using the color2D.matplot in Plotrix to plot a matrix. It works great, but there are a few things I cannot figure out (1) the value of cex.axis in the code snippet does not seem to affect the final pdf at all (at least on my system, Ubuntu 9.10, plotrix and Cairo installed from cran). How do I specify the size of the axis ticks

Hi. I have a question about the taylor.diagram() in plotrix package. How can I control the label "correlation"? In the embedded figure you can see the label "correlation" is too close to the ticks. How can I move it and make it larger? Another problem is the labels "0.95" and "0.99" are too close to the plotting area. I do not find any method to control

Hello all- I would like to orient my polar.plot (from package plotrix) so that the circular scale runs clockwise and the origin (ie. 0 degrees) starts at the top of the plot. The defaults of running the scale counter-clockwise and beginning with 90 degrees at the top of the graph seems counter-intuitive to me. I'm using R 2.5.0, and plotrix version 2.2-4. Many thanks, Tim

Hey, I hope someone is able to help. I've created a graph using kiteChart (in the plotrix package) but need to know how to perform some basic text alterations to the graph. I would like to re-orientate the text on the y-axis from vertical to horizontal. I understand that the argument normally for this is las=1. However, this does not seem to work. Perhaps kitechart uses an alternative

Hello, I am trying to use cluster.overplot from package plotrix and I get an error message when I add the "away" parameter: require(plotrix) distance <- read.table("distance.txt") cmd <- cmdscale(distance) cp <- cluster.overplot(cmd, away=2) Error in if (sum(overplots) > 1) { : missing value where TRUE/FALSE needed If I don't use "away",

Hi folks, Both plotrix and prettyR have been updated. plotrix now has the "Matlab" style dotplot that was requested not long ago on the list, provided by that intrepid duo, Barry Rowlingson and Rolf Turner. Mike Cheetham has contributed an implementation of the Piper diagram, also in response to a request. prettyR has finally learned how to display SPSS value labels in the xtab and

I am attempting to create a plot with intervals "stretched" in the x-direction using plotCI() in the plotrix package. The same data provides an appropriate set of intervals when "stretched" in the y-direction but I only get a lower interval when "stretched" in the x-direction. The data are as follows mns <-

hi all - i'm having some difficulty figuring out how to convert between "user units" (which i can't find a definition for in the plotrix package) and either (a) device units (e.g. inches with PDFs) or (b) user coordinates along any particular axis. as an example, suppose i set up a PDF device with inches, the device has both outer and inner magins, and the plot region has

I've run across what I think is a small bug in the plotrix package. I've tried to contact the maintainer (Jim Lemon) directly but email is returned 'undeliverable' at the provided address. What is the best method to push a patch to a CRAN package in this case? Thank you, Jesse

Hi My question is simple - the gap.plot function in the plotrix package allows users to draw graphs that have a broken axis. However, I want to then add a line to the "second" plot, but can't. Eg: twogrp<-c(rnorm(10)+4,rnorm(10)+20) gap.plot(twogrp,rnorm(20),gap.bounds=c(8,16),gap.axis="x",xlab="X values", xtics=c(4,7,17,20),ylab="Y

Hi, The help file for gantt.chart states that dates must be in POSIXct format, and the example shows how to do that. There's no reason that I can see that you can't use a data frame as input to gantt.chart, but you need to be very careful that your data frame matches the correct format. I bet also that your character fields were imported as factors, because you didn't specify not to.