[R] cygwin clipboard

I'd like to be able to access the windows clipboard from R under Cygwin. But... > read.table(file="clipboard") Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : unable to contact X11 display > Is this supported in any way? Thanks -Ed

Re: [R] inverse of which()

id L Carlson > Department of Anthropology > Texas A&M University > College Station, TX 77843-4352 > > -Original Message- > From: R-help On Behalf Of Ed Siefker > Sent: Wednesday, February 27, 2019 5:03 PM > To: r-help > Subject: [R] inverse of which() >

[R] inverse of which()

Given a vector of booleans, chich() will return indices that are TRUE. Given a vector of indices, how can I get a vector of booleans? My intent is to do logical operations on the output of grep(). Maybe there's a better way to do this? Thanks -Ed __

[R] How to alpha entire plot?

I have two chromatograms I want plotted on the same axes. I would like the plots to be transparent, so the first chart is not obscured. I have tried adjustcolor(..., alpha.f=0.3), the problem is that my chromatogram is so dense with datapoints that they overlap and the entire graph just ends up a

[R] Exporting to text files

I have dose response data analyzed with the package 'drc'. 'summary(mymodel)' prints my kinetic parameters. I want that text in an ASCII text file. I want to get exactly what I would get if I copied and pasted from the terminal window. I've read the documentation on data export to text files her

[R] drc, ggplot2, and gridExtra

I have dose response data I have analyzed with the 'drc' package. Using plot() works great. I want to arrange my plots and source data on a single page. I think 'gridExtra' is the usual package for this. I could use plot() and par(mfrow=...), but then I can't put the source data table on the pag

Re: [R] ggplot inside function doesn't plot

2017 at 11:54 AM, David Winsemius wrote: > >> On Nov 2, 2017, at 9:27 AM, Ed Siefker wrote: >> >> I have a function: >> >> myplot <- function (X) { >>d <- plotCounts(dds2, gene=X, intgroup="condition", returnData=TRUE) >>png(pas

[R] ggplot inside function doesn't plot

I have a function: myplot <- function (X) { d <- plotCounts(dds2, gene=X, intgroup="condition", returnData=TRUE) png(paste("img/", X, ".png", sep="")) ggplot(d, aes(x=condition, y=count, color=condition)) + geom_point(position=position_jitter(w=0.1,h=0)) + scale_y_log10

[R] googlesheets gs_reshape_cellfeed()

I have a google spreadsheet with a column of hyperlinks I want the URL from. The googlesheets package can return this information with gs_read_cellfeed(), but it needs to be reshaped with gs_reshape_cellfeed(). Problem is, gs_reshape_cellfeed() returns the 'value' of the cells, not the 'input_valu

Re: [R] as.data.frame doesn't set col.names

; "geno" Really, really confused. On Tue, Oct 24, 2017 at 12:58 PM, Ed Siefker wrote: > Why doesn't this work? > >> samples$geno <- as.data.frame(sapply(yo, toupper), col.names="geno") >> samples > quan

[R] as.data.frame doesn't set col.names

Why doesn't this work? > samples$geno <- as.data.frame(sapply(yo, toupper), col.names="geno") > samples quant_samples age sapply(yo, toupper) E11.5 F20het BA40 E11.5 F20het BA40 E11.5 F20HET E11.5 F20het BA45 E11.5 F20het BA45 E11.5 F20

[R] A list of data frames and a list of colnames.

I have a list of file names, and a list of data frames contained in those files. mynames <- list.files() mydata <- lapply(mynames, read.delim) Every file contains two columns. > colnames(mydata[[1]]) [1] "Name" "NumReads" > colnames(mydata[[2]]) [1] "Name" "NumReads" I can set the colna

[R] data.matrix output is not numeric

I have a data frame full of integer values. I need a matrix full of numeric values. ?data.matrix reads: Return the matrix obtained by converting all the variables in a data frame to numeric mode and then binding them together as the columns of a matrix. This does not work. test.

[R] Fwd: Boxplot, formula interface, and labels.

..@r-project.org] On Behalf Of Ista Zahn > Sent: Thursday, September 28, 2017 12:27 PM > To: Ed Siefker > Cc: r-help > Subject: Re: [R] Boxplot, formula interface, and labels. > > mybp <- boxplot(count ~ geno * tissue, data = mydata, plot = FALSE) > mybp$names <- gsub

Re: [R] Boxplot, formula interface, and labels.

t()? On Thu, Sep 28, 2017 at 11:40 AM, Ed Siefker wrote: > I have data I'd like to plot using the formula interface to boxplot. > I call boxplot like so: > > with(mydata, boxplot(count ~ geno * tissue)) > > I get a boxplot with x axis labels like "wt.kidney". I w

[R] Boxplot, formula interface, and labels.

I have data I'd like to plot using the formula interface to boxplot. I call boxplot like so: with(mydata, boxplot(count ~ geno * tissue)) I get a boxplot with x axis labels like "wt.kidney". I would like to change the '.' to a newline. Where is this separator configured? Thanks, -Ed _

[R] T tests on multiple groups

I have a data set with observations on groups with multiple variables. Let's call them GENO and AGE. I have control and test genotypes and two different ages. It is only meaningful to compare control and test within the same age. I'd like to get the p value for each group compared back to contro

Re: [R] merging dataframes in a list

package to bind all the data.frames together > (a regular loop will also work). Afterwards you can summarise using ddply > > Hope this helps > Ulrik > > > Ed Siefker schrieb am Fr., 3. Juni 2016 21:10: >> >> aggregate isn't really what I want. Maybe tapply? I

Re: [R] merging dataframes in a list

ata type. What function will do the same on lists? lapply doesn't have a 'by' argument. On Fri, Jun 3, 2016 at 1:41 PM, Ed Siefker wrote: > I manually constructed the list of sample names and tried the > aggregate call I mentioned. > Merge works when called manually, b

Re: [R] merging dataframes in a list

ame red green 1 sample2 1030 > aggregate(mylist, by=as.list(names), merge) Error in as.data.frame(y) : argument "y" is missing, with no default What's the right way to do this? On Fri, Jun 3, 2016 at 1:20 PM, Ed Siefker wrote: > I have a list of data as follo

[R] merging dataframes in a list

I have a list of data as follows. > list(data.frame(name="sample1", red=20), data.frame(name="sample1", > green=15), data.frame(name="sample2", red=10), data.frame(name="sample 2", > green=30)) [[1]] name red 1 sample1 20 [[2]] name green 1 sample115 [[3]] name red 1 sample

[R] reading data into nested frames

I have many data files named like this: E11.5-021415-dko-1-1-masked-bottom-area.tsv E11.5-021415-dko-1-1-masked-top-area.tsv E11.5-021415-dko-1-2-masked-bottom-area.tsv E11.5-021415-dko-1-2-masked-top-area.tsv E11.5-021415-dko-1-3-masked-bottom-area.tsv E11.5-021415-dko-1-3-masked-top-area.tsv ag

[R] lists and rownames

I'm doing some string manipulation on a vector of file names, and noticed something curious. When I strsplit the vector, I get a list of character vectors. The list is numbered, as lists are. When I cast that list as a data frame with 'as.data.frame()', the resulting columns have names derived fr

Re: [R] aggregate and the $ operator

So that's how that works! Thanks. On Fri, Jan 22, 2016 at 1:32 PM, Joe Ceradini wrote: > Does this do what you want? > > aggregate(Nuclei ~ Slide, example, sum) > > On Fri, Jan 22, 2016 at 12:20 PM, Ed Siefker wrote: >> >> Aggregate does the right thing w

[R] aggregate and the $ operator

Aggregate does the right thing with column names when passing it numerical coordinates. Given a dataframe like this: Nuclei Positive Nuclei Slide 1133 96A1 2 96 70A1 3 62 52A2 4 60 50A2 I can call 'aggregate' li

[R] plot changes usr?

I'm trying to plot() over an existing plot() like this: > attach(mtcars) > plot(mpg, hp) > par(new=TRUE) > par("usr") [1] 9.46 34.84 40.68 346.32 > plot(mpg, hp, col="red", axes=FALSE, xlim=par("usr")[1:2], > ylim=par("usr")[3:4], xlab="", ylab="") > par("usr") [1] 8.4448 35.8552 28.4544

[R] Java requested System.exit(130)

I'm used to using ctrl-c to end operations without killing R. But I've used xlsx in this session, which loads Java, which apparently intercepts the ctrl-C. Accordingly, I hit ctrl-C, R died, and I lost a lot of work. I did some looking, and found a thread(http://comments.gmane.org/gmane.comp.lan

[R] why is this a factor?

I have a table, and I want a new column to add some annotations to. But it ends up as a factor instead of characters, and won't let me add arbitrary text. > data(iris) > iris<-data.frame(iris,annot=c("")) > iris[1,"annot"]<-"annotation" Warning message: In `[<-.factor`(`*tmp*`, iseq, value = "anno

Re: [R] Why do I have a column called row.names?

-- > David L Carlson > Associate Professor of Anthropology > Texas A&M 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 Ed Sief

[R] Why do I have a column called row.names?

I'm trying to read in a tab separated table with read.delim(). I don't particularly care what the row names are. My data file looks like this: start stopSymbol Insert sequence Clone End Pair FISH 203048 67173930ABC8-43024000D23TI:993812543 TI:993834585 255176 87

Re: [R] lapply and paste

lapply -- paste is > vectorized so this > > paste("filename_", suff, ".ext", sep = "") > > will work. But if you want to use lapply (for whatever reason) try this: > > lapply(suff, function(x) paste("filename_", x, ".ext", sep = &q

[R] lapply and paste

I have a list of suffixes I want to turn into file names with extensions. suff<- c("C1", "C2", "C3") paste("filename_", suff[[1]], ".ext", sep="") [1] "filename_C1.ext" How do I use lapply() on that call to paste()? What's the right way to do this: filenames <- lapply(suff, paste, ...) ? Can

[R] avoiding for loops

I have data that looks like this: > df1 group id 1 red A 2 red B 3 red C 4 blue D 5 blue E 6 blue F I want a list of the groups containing vectors with the ids.I am avoiding subset(), as it is only recommended for interactive use. Here's what I have so far: df1 <- data.fra

Re: [R] argument names inside a function?

Thanks, deparse(substitute()) does exactly what I want. On Sat, Mar 24, 2012 at 4:20 PM, R. Michael Weylandt wrote: > Can you be a little more concrete? > > If you want the form of the expression given (rather than its value), > deparse(substitute()) will work: > > fnc1 <- function(x){ deparse(su

[R] argument names inside a function?

Is there a way I can get the names of the arguments passed to a function from within a function? __ 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.htm

[R] subsetting by cell value with a list

I would like to subset by dataframe by matching all rows that have any value from a list of values. I can get it to work if I have exactly one value, I'm not sure how to do it with a list of values though. This works and gives me exactly one line: my.df[ which( mydf$IDX==17)), ] I would like to

[R] Rserve as a proxy

Is there a simple way to use Rserve/RSclient as a proxy to transparently send requests from a local instance of R to a remote instance? It seems like this would by doable by wrapping each call that doesn't refer to a local path inside RSeval. Is this harder than it seems? Does this already exis

[R] logical to vector?

I am trying to use the coXpress function from the coXpress package. This function requires numerical vectors indicating which columns are in which group. The problem is, I can only figure out how to get a logical structure, not a numerical one. In other words, coXpress wants something like: "1:3"