[R] numeric comparison error

Hi, I am a little bit perplexed at why I am getting some values as FALSE: > cpgbins <- seq(0,1,0.05) > cpgbins [1] 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 > cpgbins[1] == 0.00 [1] TRUE > cpgbins[2] == 0.05 [1] TRUE > cpgbins[3] =

[R] grep

Hi, I was trying to find a pattern ("ABHD14A") in a character string ('xgen' in example below) using grepl. Note that the individual members may be separated by a semi-colon. The correct answer should return: "ABHD-ACY1 ; ABHD14A" "ABHD14A ; YYY" I have tried three approaches, but still seem a

[R] Jagged ROC curves?

Hi, I was trying to draw some ROC curves (prediction of case/control status), but seem to be getting a somewhat jagged plot. Can I do something that would 'smooth' it somewhat? Most roc curves seem to have many incremental changes (in x and y directions), but my plot only has 4 or 5 steps even tho

Re: [R] Jagged ROC curves?

i', ylab='', xlab='') plot(smooth(roc_1),col="brown3", lwd=2, add=T, lty=1) I guess most ROCs that I've seen are somewhere in between, i.e. they have a little jaggedness, but not as much as in plot #1 above" thanks! On Mon, Jun 26, 2017 at 12:59 PM, Marc S

[R] ggplot2 geom_bar arrangement

Hi, I was trying to draw a geom_bar plot. However, by default, the bars are arranged according to the label, which I don't want. I want the bars to appear exactly as they appear in the data frame. For example in the code: Lab=c(letters[4:6],letters[1:3]) valuex = c(3.1,2.3,0.4,-0.4,-1.2,-4.4)

[R] ggplot2 geom_bar label justification

Hi, I was trying to make a horizontal bar plot. The barplot works when the text labels are of reasonable length, but not if some of them are slightly long. I think the long ones get 'squeezed' by default before the plot is flipped and keep the skew after the flip. Is there a way I can get around t

Re: [R] ggplot2 geom_bar arrangement

; > # set the factor levels to the same order as observed in the data frame > df$Lab <- factor(df$Lab, levels=unique(df$Lab)) > > px <- ggplot(df,aes(Lab,valuex,label=Lab)) + > geom_text(aes(y=0)) + > geom_bar(stat = "identity") > px > > Jean > >

[R] par(mfrow) for heatmap plots

Hi, I was trying to use par(mfrow) to put 4 heatmaps on a single page. However, I get one plot per page and not one page with 4 plots. What should I modify? Test code is given below: test = matrix(rnorm(60), 20, 3) pdf(file='test.pdf',width=10,height=8) par(mfrow=c(2,2)) heatmap(test) heatmap(te

[R] plot: rug colors

Hi, I wanted the rug (in plot) to have different colors. For example: vals1 <- sample(1:100,5) vals2 <- sample(1:100,5) rugcols <- c("red","blue","brown","red","yellow") plot(vals1,vals2) rug(vals1,col=rugcols,lwd=2) However, with this code I only get 'red' for all the ticks. Is there a way I

Re: [R] plot: rug colors

Thanks Duncan! That works! On Sun, May 24, 2015 at 8:09 AM, Duncan Murdoch wrote: > On 24/05/2015 7:47 AM, Brian Smith wrote: > > Hi, > > > > I wanted the rug (in plot) to have different colors. For example: > > > > vals1 <- sample(1:100,5) > > vals2 &l

[R] read.table - replaces 'T' with 'TRUE'

Hi, I had a table with 'T's in it. When I try to read the table, it replaces all the 'T's with TRUE. Is there a way that I can retain the Ts? thanks! Sample table (test.txt): xx1 xx2 0 0 2 2 A A G G A G A A C C G G G G G G A G A A A G A G A A G G A A A G G G A G A G G G A G A G G G G G A G G G

Re: [R] read.table - replaces 'T' with 'TRUE'

Thanks!! On Mon, Jan 26, 2015 at 5:23 PM, peter dalgaard wrote: > > > On 26 Jan 2015, at 23:10 , Duncan Murdoch > wrote: > > > > read.table(, colClasses = "character") > > > > (You might want "factor" instead of character.) > > Or maybe not. I'd expect trouble with getting the levels set to > c

[R] ggplot2 boxplot points (size,color,shape)

Hi, I am trying to create a boxplot (with geom_jitter) such that the points from one set of values are shown as circles, and the second set of points also as circles, but with no fill. In other words, how can I control the shape and color for the points appearing in this boxplot? === library(

[R] hash - extract key values

Hi, I was trying to use hash, but can't seem to get the keys from the hash. According to the hash documentation ('hash' package pdf, the following should work: > hx <- hash( c('a','b','c'), 1:3 ) > class(hx) [1] "hash" attr(,"package") [1] "hash" > hx$a [1] 1 > keys(hx) Error in (function (classe

Re: [R] hash - extract key values

gt; keys(hx) > [1] "a" "b" "c" > > > Maybe restart your session? Clear your workspace? Upgrade? > > B. > > > > > > On Mar 27, 2015, at 7:39 PM, Brian Smith wrote: > > > Hi, > > > > I was trying to use hash, bu

Re: [R] hash - extract key values

ics grDevices utils datasets methods base other attached packages: [1] hash_3.0.1 loaded via a namespace (and not attached): [1] tools_3.1.2 > On Sat, Mar 28, 2015 at 5:02 AM, Uwe Ligges wrote: > Try to reinstall hash. Sounds like a broken installation. > > Best, > Uwe Ligge

Re: [R] hash - extract key values

t; Then there will be 26 items in the hash table and keys(yourhash) > will return the 26 lowercase letters. Is that what you want? > > Bill Dunlap > TIBCO Software > wdunlap tibco.com > > On Sat, Mar 28, 2015 at 2:56 PM, Brian Smith > wrote: > >> I deleted t

[R] ggplot: connect points with line (not in order)

Hi, I am trying to connect points, but not in a different order than the default value in ggplot. For example: xx <- sample(1:100,5) yy <- sample(1:100,5) mydat <- data.frame(xx,yy) print(mydat) ggplot(mydat,aes(xx,yy)) + geom_point() + geom_line() I want to connect the points as the

Re: [R] ggplot: connect points with line (not in order)

ts-in-ggplot2-in-r > > > > -- > | > > http://billyam.com || http://use-r.com || http://shinyserver.com (BETA) > > SAS Certified Base Programmer for SAS 9 > Oracle SQL Expert(11g) > > > > On Sun, Apr 5, 2015 at 9:03 PM, Brian Smith > wrote: > > Hi

[R] package multicore: check progress?

Hi, I use multicore package quite a lot. However, I want to find a way to check on the progress of my job. For example: ftest <- function(x){ if(x %% 100 == 0) print(x) y <- 2x return(y) } res <- mclapply(1:1000,ftest) This would print the value of x in a for loop, but doesn't produce anythin

[R] ggplot2: Controlling width of line

Hi, I was trying to increase the size of certain lines in my plot (samples 'B' and 'D' in example below). However, when I try to modify the line size, I seem to screw up the linetypes. Also, is there a way to reflect the line size in the legend? Here is some sample code for illustration: library

[R] ggplot2: remove axis ticks

Hi, I was trying to remove the axis tick marks and their values using theme() but haven't had much success. Here is sample code: rx <- sample(1:100,10) ry <- sample(1:100,10) rz <- sample(letters[1:3],10,replace=T) rdf <- data.frame(rx,ry,rz) p <- ggplot(rdf,aes(x=rx,y=ry)) p1 <- p + geom_point(

[R] ChAMP: champ.runCombat error with methylation 450k data

Hi, I was trying to run COMBAT on methylation data, but keep on getting an error: Error in while (change > conv) { : missing value where TRUE/FALSE needed The error occurs irrespective of whether I give the entire or reduced (variation filter keeps only about 140k CpGs) datasets. Is there any o

[R] x-axis tick marks on log scale plot

Hi, I have a plot with log scale on the axes. How do I add ticks and labels in addition to the ones provided by default? Can I specify where I want the ticks and labels? For example: set.seed(12345) x <- sample(1:1,10) y <- sample(1:1,10) plot(x,y,log="xy") For me, this plot has tick

Re: [R] x-axis tick marks on log scale plot

> -- > https://www.researchgate.net/profile/Ivan_Calandra > https://publons.com/author/705639/ > > > Le 19/05/2016 à 15:40, Brian Smith a écrit : > >> Hi, >> >> I have a plot with log scale on the axes. How do I add ticks and labels in >> addition to th

[R] Using R to analyse Court documents

Hi, I am wondering if there is some references on how R can be used to analyse legal/court documents. I searched a bit in internet but unable to get anything meaningful. Any reference will be very appreciated. Thanks for your time. Thanks and regards, __

[R] igraph: layout help

Hi, I was trying to make a network plot of this data: library(igraph) library(network) df1 <- data.frame(from="A",to=c("B","C","D","E","F","G"),value=1) df2 <- data.frame(from="K",to=c("L","M","N"),value=1) df3 <- data.frame(from="A",to="K",value=3) my.df <- rbind(df1,df2,df3) my.g

[R] Could you manually replicate execution of a R function

Hi, I have trying to replicate a function from rugarch package manually. Below is the calculation based on the function, library(rugarch) data(dji30ret) spec = ugarchspec(mean.model = list(armaOrder = c(1,1), include.mean = TRUE), variance.model = list(model = "gjrGARCH"), distribution.model = "s

[R] Unable to manually replicate execution of a R function

Hi, ** In may earlier post there were some typo, so reposting the same after correction** I am trying to replicate a function from rugarch package manually. Below is the calculation based on the function, library(rugarch) data(dji30ret) spec = ugarchspec(mean.model = list(armaOrder = c(1,1), inc

Re: [R] Could you manually replicate execution of a R function

Hi Ivan, Thanks for pointing this out. It now matches. Thanks and regards, On Thu, 21 Sept 2023 at 13:04, Ivan Krylov wrote: > > On Tue, 19 Sep 2023 23:09:18 +0530 > Brian Smith wrote: > > > C = rep(0, length(D)) > > N = length(D) > > In the VaRDurTest fun

[R] Manually calculating values from aov() result

Hi, I have performed ANOVA as below dat = data.frame( 'A' = c(-0.3960025, -0.3492880, -1.5893792, -1.4579074, -4.9214873, -0.8575018, -2.5551363, -0.9366557, -1.4307489, -0.3943704), 'B' = c(2,1,2,2,1,2,2,2,2,2), 'C' = c(0,1,1,1,1,1,1,0,1,1)) summary(aov(A ~ B * C, dat)) However now I also trie

Re: [R] Manually calculating values from aov() result

Hi, Thanks for this information. Is there any way to force R to use Type-1 SS? I think most textbooks use this only. Thanks and regards, On Wed, 7 Aug 2024 at 17:00, Duncan Murdoch wrote: > > On 2024-08-07 6:06 a.m., Brian Smith wrote: > > Hi, > > > > I have

Re: [R] about mix type clust algorithm

Thanks for the article, Jose! It looks very interesting. On Mon, Jul 22, 2013 at 7:12 AM, Jose Iparraguirre < jose.iparragui...@ageuk.org.uk> wrote: > Dear Cheng, > > This question exceeds the topics of this group. However, you may benefit > from this recent (and excellent) paper along with the

[R] write.table and append

Hi, I am trying to append tables on file with this sample code: for(i in 1:2){ mat <- data.frame(sample(1:30,9),3,3) colnames(mat) <- letters[1:3] ifelse(i == 1,write.table(mat,paste('test.txt',sep=''),row.names=F), write.table(mat,paste('test.txt',sep

Re: [R] write.table and append

> } else { > > write.table(mat,paste('test.txt',sep=''),row.names=F,col.names=F,append=TRUE) > } > } > > Hope that helps, > > Louis > > > On Fri, Feb 8, 2013 at 2:40 PM, Brian Smith > wrote: > > > > Hi, > > &

Re: [R] write.table and append

Ah, I didn't know this! Thanks Ben. On Fri, Feb 8, 2013 at 10:18 AM, Ben Tupper wrote: > Hi, > > On Feb 8, 2013, at 9:40 AM, Brian Smith wrote: > > > Hi, > > > > I am trying to append tables on file with this sample code: > > > >for(i in

[R] Changing default order of plots in par

Hi, I wanted to change the order of how the plots appear in a multiplot scenario. For example, in the code below: # pdf('test.pdf',width=8,height=8) par(mfrow = c(2,2)) for(i in 1:2){ v1 <- sample(1:1000,50) v2 <- sample(1:1000,50) mat <- cbind(v1,v2) plot(v1,v2) boxplot(mat) }

Re: [R] Changing default order of plots in par

Thanks Rui! That worked. On Sat, Mar 9, 2013 at 4:22 PM, Rui Barradas wrote: > Hello, > > Instead of mfrow use mfcol and the order becomes col by col. > > Hope this helps, > > Rui Barradas > > Em 09-03-2013 20:55, Brian Smith escreveu: > >> Hi, >>

[R] Testing for significance of overlap in three sets - mantelhaen test?

Hi, My apologies for the naive question! I have three overlapping sets and I want to find the probability of finding a larger/greater intersection for 'A intersect B intersect C' (in the example below, I want to find the probability of finding more than 135 elements that are common in sets A, B &

[R] Creating a hyperlink in a csv file

Hi, I was wondering if it is possible to create a hyperlink in a csv file using R code and some package. For example, in the following code: links <- cbind(rep('Click for Google',3),"http://www.google.com";) write.table(links,'test.csv',sep=',',row.names=F,col.names=F) the web address should be

[R] Writing a hyperlink to a csv file

Hi, I was wondering if it is possible to create a hyperlink in a csv file using R code and some package. For example, in the following code: links <- cbind(rep('Click for Google',3),"google search address goes here") ## R Mailing list blocks if I put the actual web address here write.table(links,

Re: [R] Writing a hyperlink to a csv file

xt file so that excel recognizes it as hyperlinked text. Does that make sense? thanks! On Sat, Mar 16, 2013 at 4:16 AM, Marc Girondot wrote: > Le 15/03/13 12:53, Brian Smith a écrit : > > Hi, >> >> I was wondering if it is possible to create a hyperlink in a csv file >

[R] scatterplot3d with densCols ?

Hi, I was trying to make a 3D plot using densCols. The documentation for densCols doesn't look like it'll work for 3D. For example: - library(scatterplot3d) v1 <- rnorm(1) v2 <- rnorm(1) v3 <- rnorm(1) ## 2D with denscols mat1 <- cbind(v1,v2)

Re: [R] scatterplot3d with densCols ?

lor', not 'col'. > > scatterplot3d(mat,color=mcols,**pch=16) > > HTH, > Pascal > > > > On 28/03/13 19:41, Brian Smith wrote: > >> Hi, >> >> I was trying to make a 3D plot using densCols. The d

[R] Selecting divergent colors

Hi, I was trying to make a density plot with 13 samples. To distinguish each sample, it would be good if each color is as different as possible from the other colors. I could use the built in function, but that does not do more than 8 colors and then goes back to recycling the cols. If I use a pal

[R] ggplot2 error: "Error in as.environment(where) : 'where' is missing"

Hmm...I think it used to work before, but it gives an error now. Here is some sample code: = library(ggplot2) Sample <- rep(c('A','B'),rep(10,2)) Vals <- sample(1:1000,20) dataf <- as.data.frame(cbind(Sample,Vals)) myplot <- ggplot(dataf,aes(x=Vals,colour=Sample)) + geom_density() mypl

Re: [R] ggplot2 error: "Error in as.environment(where) : 'where' is missing"

s) > str(dataf) > #'data.frame':20 obs. of 2 variables: > # $ Sample: Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1 ... > # $ Vals : int 96 712 765 121 154 78 821 258 812 51 ... > > ggplot(dataf,aes(x=Vals,colour=Sample))+geom_density() #no error

[R] boxplot axis font size

Hi, I wanted to have a different font for my x-axis and y-axis. How can I use the par function to specify different font sizes for x and y axis? For example: x <- matrix(rnorm(2000),200,10) colnames(x) <- letters[1:10] par(cex.axis=0.5) boxplot(x,cex=0.2) But this sets the font size to 0.5 for b

[R] Basic plot density question

Hi, I wanted to plot two different density profiles. My code looks like: x1 <- rnorm(100,mean=0,sd=1) x2 <- rnorm(100,mean=1,sd=1) plot(density(x1),xlab="",col="red",main="") par(new=T) plot(density(x2),xlab="",col="blue",main="") However, the x-axis values don't match up for the two plots. I

Re: [R] Basic plot density question

range(d1$y,d2$y), > xlim=range(d1$x,d2$x) ) > lines(d2, col='blue') > > Other options include the matplot function or tools in the lattice and > ggplot2 packages. > > On Wed, Jun 18, 2014 at 8:48 AM, Brian Smith > wrote: > > Hi, > > > > I wa

[R] Question on 'get'

Hi, I was trying to get at some values from 'data' using the get function. Here is my code: > class(data) [1] "data.frame" > class(data$gender.factor) [1] "factor" > head(data$gender.factor) [1] Male Female Male Female Male Female Levels: Male Female > xx <- get("data$gender.factor") Error

[R] lapply?

Hi, I was trying to use lapply to create a matrix from a list: uu <- list() uu[[1]] <- c(1,2,3) uu[[2]] <- c(3,4,5) The output I desire is a matrix with 2 rows and 3 columns, so I try: xx <- lapply(uu,rbind) Obviously, I'm not doing something right, but what!? [[alternative HTML versi

Re: [R] lapply?

Thanks all! So many ways On Thu, Nov 14, 2013 at 10:35 AM, Rui Barradas wrote: > Hello, > > You are applying rbind to each element of the list, not rbinding it with > the others. Try instead > > do.call(rbind, uu) > > Hope this helps, > > Rui Barradas > &

[R] linear model lme4

Hi, I wanted to check the difference in results (using lme4) , if I treated a particular variable (beadchip) as a random effect vs if I treated it as a fixed effect. For the first case, my formula is: lmer.result <- lmer(expression ~ cancerClass + (1|beadchip)) For the second case, I want t

[R] linear model - lm (Adjusted R-squared)?

Hi, Sorry for the naive question, but what exactly does the 'Adjusted R-squared' coefficient in the summary of linear model adjust for? Sample code: > x <- rnorm(15) > y <- rnorm(15) > lmr <- lm(y~x) > summary(lmr) Call: lm(formula = y ~ x) Residuals: Min 1Q Median 3Q Max -1

[R] Installing Rmpi on hpc

Hi, I was trying to install the package Rmpi on a hpc cluster running SGE. The command, and the sessionInfo() is as follows: === > install.packages("Rmpi",dependencies=TRUE) also installing the dependency ‘rsprng’ trying URL ' http://www.ibiblio.org/pub/la

[R] ggplot geom_freqpoly() layers ..?

Hi, I was trying to overlay/combine two freqpoly plots. The sample code below illustrates the problem. Essentially, I want to do is: 1. Have the same colour for all the lines in 'Plot 1' (and 'Plot 2'). Currently, all the lines in Plot 1 have different colours and all the lines in Plot 2 have dif

Re: [R] ggplot geom_freqpoly() layers ..?

colour for the second set of distributions. Does that make sense? thanks! On Thu, Sep 8, 2011 at 11:26 AM, Ista Zahn wrote: > Hi Brian > > On Thu, Sep 8, 2011 at 10:30 AM, Brian Smith > wrote: > > Hi, > > > > I was trying to overlay/combine two freqpol

[R] ggplot2: legend for geom_rug() ..?

Hi, I was trying to make another legend for the rug plot. Sample code: library(ggplo2) ids <- paste('id_',1:3,sep='') before <- sample(9) after <- sample(1:10,9) dat <- as.matrix(cbind(before,after)) rownames(dat) <- rep(ids,3) position <- c(rep(10,3),rep(13,3),rep(19,3)) mdat <- cbind(melt(dat

[R] Lattice/"panel.bwplot" and Gviz: Boxplot question

Hi, I was using Gviz package to create a boxplot. I understand that Gviz uses "panel.bwplot" to create the boxplot. Is there any way that I can remove the dashed line surrounding each pair of boxplots? Here is some sample code: # library(Gviz) thisdata <- matrix(sample(1:100,60),n

[R] ggplot2: changing default colors of boxplot

Hi, I wanted to change the default colors appearing in boxplot. For example, the following code (from the package/documentation): === library(ggplot2) p <- ggplot(mtcars, aes(factor(cyl), mpg)) p + geom_boxplot(aes(fill = factor(am))) === Gives the default colors. What do I nee

[R] Reading data with 'awk' - basics?

Hi, I had a large file for which I require a subset of rows. Instead of reading it all into memory, I use the awk command to get the relevant rows. However, I'm doing it pretty inefficiently as I write the subset to disk, before reading it into R. Is there a way that I can read it into an R object

Re: [R] Reading data with 'awk' - basics?

Got it. Thanks! On Mon, Oct 17, 2011 at 9:40 AM, Prof Brian Ripley wrote: > On Mon, 17 Oct 2011, Brian Smith wrote: > > Hi, >> >> I had a large file for which I require a subset of rows. Instead of >> reading >> it all into memory, I use the awk command to

[R] Simple color strip

Hi, I was trying to get an image/pdf of a sequence of colors in the order given. For example: myCols <- c('#BF','#BF','#FF','#FF','#BF','#FF') I'd like to make a strip of colors as they appear in the order above and save it as a pdf file. Is there a function in the base

Re: [R] Simple color strip

0BF','#** >> FF') >> >> >> I'd like to make a strip of colors as they appear in the order above and >> save it as a pdf file. Is there a function in the base package (or some >> other package) to do this? >> >> > On 19/1

[R] ggplot2: scale_shape_manual

Hi, I was trying to replicate one of the graphs given on the ggplot2 website. I have given a sample code below. I would like to combine the legends, since each color is uniquely mapped to a shape. ### library(ggplot2) leaves <- letters[1:8] mat <- matrix(sample(1:1000,32),nrow=16,nco

Re: [R] ggplot2: scale_shape_manual

t(aes(colour = factor(leaves),size=3)) + scale_shape_manual(values=vals) = thanks! On Mon, Apr 16, 2012 at 3:09 PM, Brian Diggs wrote: > On 4/16/2012 7:31 AM, Brian Smith wrote: > >> Hi, >> >> I was trying to replicate one of the graphs given on the ggplot2 webs

[R] Modifying R package code

Hi, I was trying to change some code in an existing package. I downloaded the source package (say 'package_xx') from CRAN, and changed the R code provided in the /package_xx/R/xx.R. I then saved the changes and did the R CMD INSTALL -l /path to modified package/. Do I need to do something else be

[R] ggplot2: Dendrogram text position

Hi, I was trying to create a dendrogram using ggplot2. Everything seems to be looking ok except that the text labels are too close to the dendrogram (in the example below, 'a','b', ..). Is there a way that I can put a little gap between where the dendrogram ends and the label begins? thanks!! ==