?scale_x_discrete, in particular the expand argument.
On June 19, 2020 7:07:32 PM PDT, Rolf Turner wrote:
>
>I'm having trouble adjusting axis limits in ggplot2 when the variable
>corresponding to that axis is a factor. I have attached a minimal
>reproducible example in the file demo.txt.
>
I'm having trouble adjusting axis limits in ggplot2 when the variable
corresponding to that axis is a factor. I have attached a minimal
reproducible example in the file demo.txt.
The result (see it by sourcing demo.txt and printing ldCiPlot) is fine
except that I would like the y-axis limits
All of your torrent of requests for help to have others do your work for
you are about genomics issues. Why aren't you posting on the Bioconductor
Help forum instead, where both the expertise and tools for such matters
exist? I would characterize your posts here as being largely inappropriate
for
unfortunately it complains again:
> f1 <- read_tsv("1g", col_names=F)
Parsed with column specification:
cols(
X1 = col_character()
)
> f2 <- read_tsv("1n", col_names=F)
Parsed with column specification:
cols(
X1 = col_character()
)
> for ( a in rownames(f1) ) {
+
+for ( b in rownames(f2)
Hi Rasmus,
I got those SNPs from two GWAS-es which I run with different
phenotypes and I would like to compare weather the top SNPs in both of
them are in LD.
So 1n.txt and 1g.txt are just top SNPs from those two GWAS-es.
Unfortunately https://ldlink.nci.nih.gov/?tab=ldpair works for only
two
Thank you all for the responses, these are the insights I was hoping for.
There are many ways to get this right, and I happened to run into one that
has a glitch. I see from Luke's explanation how the strange output came
about. Glad to hear that this bug/behavior is already known.
On Fri, Jun 19,
On 2020-06-19 14:34 -0500, Ana Marija wrote:
>
> I have two files (each has 300 lines)like this:
The example looks quite similar to the R example in
https://rest.ensembl.org/documentation/info/ld_pairwise_get#ra
...
The question becomes: how did you query the
600 variant names in 1g.txt and
If I understand your question correctly, you're already able to read
an EPS file.
So, essentially, you have an answer to your question.
Paul Murrell published an article on using raster graphics, in 2011.
https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Murrell.pdf
I would assume
On 6/19/2020 5:49 AM, Sébastien Lahaie wrote:
I ran into some strange behavior in R when trying to assign a treatment to
rows in a data frame. I'm wondering whether any R experts can explain
what's going on.
First, let's assign a treatment to 3 out of 10 rows as follows.
df <- data.frame(unit
Sorry - its been a long week!
there is a foreach package but I try to avoid extras
make your for statements:
for ( a in rownames(f1) ) {
# a will now be a row number rather than the value, so replace ' a ' in
the paste0 with: f1[ a, 1]
so
ext <- paste0( "/ld/human/pairwise/",
Dear other list readers,
On 2020-06-19 23:31 +0200, Rasmus Liland wrote:
> I have attached my rds here.
only Ana recieved this because of a Mailman
attachment policy, which also is why my
signature was bad ...
Best,
Rasmus
signature.asc
Description: PGP signature
I tried it:
> library(httr)
> library(jsonlite)
> library(xml2)
> library(readr)
> server <- "http://rest.ensembl.org;
> f1 <- read_tsv("1g", col_names=F)
Parsed with column specification:
cols(
X1 = col_character()
)
> f2 <- read_tsv("1n", col_names=F)
Parsed with column specification:
cols(
Oh - read.text isn't in base! Not sure where is came from (my head
mostly!) You may have something that adds it but better to use
something that works. So try using:
library(readr)
f1 <- read_tsv("1g.txt", col.names=F)
This will give you a tibble with f1$X1 with the file in it
then loop
On 2020-06-19 16:07 -0500, Ana Marija wrote:
> HI Rasmus,
>
> I tried it:
>
> library(base)
>
> > r <- readRDS(paste0(population.name, ".rds"))
> Error in gzfile(file, "rb") : cannot open the connection
> In addition: Warning message:
> In gzfile(file, "rb") :
> cannot open compressed file
HI Rasmus,
I tried it:
library(base)
files <- c("1g.txt", "1n.txt")
files <- lapply(files, readLines)
server <- "http://rest.ensembl.org;
population.name <- "1000GENOMES:phase_3:KHV"
ext <- apply(expand.grid(files), 1, function(x) {
Hi,
thanks for getting back to me, it is just for my job :)
so I tried it:
library(httr)
library(jsonlite)
library(xml2)
library(SparkR, lib.loc = c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib")))
sparkR.session(master = "local[*]", sparkConfig =
list(spark.driver.memory = "2g"))
server <-
On 2020-06-19 14:34 -0500, Ana Marija wrote:
>
> server <- "http://rest.ensembl.org;
> ext <-
> "/ld/human/pairwise/rs6792369/rs1042779?population_name=1000GENOMES:phase_3:KHV"
>
> r <- GET(paste(server, ext, sep = ""), content_type("application/json"))
>
> stop_for_status(r)
>
so (untested) if you did something like
f1 <- read.text("1g.txt")
f2 <- read.text("1n.txt")
for ( a in as.list(f1) ) {
for ( b in as.list(f2) ) {
ext <- paste0( "/ld/human/pairwise/",
a,
"/",
b,
Hello,
I have two files (each has 300 lines)like this:
head 1g.txt
rs6792369
rs1414517
rs16857712
rs16857703
rs12239392
...
head 1n.txt
rs1042779
rs2360630
rs10753597
rs7549096
rs2343491
...
For each pair of rs# from those two files I can run this command in R
library(httr)
library(jsonlite)
The behavior has been there much longer than that in R and it's been a
known issue with complex assignment for a long time (not the only
one). You're in a better position than I to know how Splus handles this.
The complex assignment expression
df[, ]$treated <- TRUE
is basically evaluated
Hi All,
We need to get clarification from Kristin as to what kinds of issues are raised
in the context of a risk analysis from her IT people.
Since Kristin's wording indicated:
"...all programs that our employees/providers use must be vetted through the
IT Department by way of a Risk
It is a bug that has been present in R since at least R-2.14.0 (the oldest
that I have installed on my laptop).
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Jun 19, 2020 at 10:37 AM Rui Barradas wrote:
> Hello,
>
>
> Thanks, I hadn't thought of that.
>
> But, why? Is it evaluated once
Hello,
Thanks, I hadn't thought of that.
But, why? Is it evaluated once before assignment and a second time when
the assignment occurs?
To trace both sample and `[<-` gives 2 calls to sample.
trace(sample)
trace(`[<-`)
df[sample(nrow(df), 3),]$treated <- TRUE
trace: sample(nrow(df), 3)
Hi Jeff,
I tried to reproduce your problem with the package's example and I did
not get an error.
Here's the output from my sessionInfo().
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS
Matrix products: default
BLAS:
OS? R version? package versions?
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Fri, Jun 19, 2020 at 10:02 AM Jeff Reichman
wrote:
> r-help
>
>
>
> I'm
r-help
I'm trying to use the TSstudio library to plot a forecast created from a
Holt Winters model and I get the following error:
Error in `[<-`(`*tmp*`, n + 1, , value = data.frame(x = tmp[["x"]][n], :
subscript out of bounds
So looking through the package documentation I tried
I think the question of validation is very different from the risk analysis
referenced in the subject line.
On the subject of the FDA accepting open source software. Personally I've
done two sBLA submissions where simulation results were essential aspects
of the filings. Both were approved and
The first subscript argument is getting evaluated twice.
> trace(sample)
> set.seed(2020); df[i<-sample(10,3), ]$Treated <- TRUE
trace: sample(10, 3)
trace: sample(10, 3)
> i
[1] 1 10 4
> set.seed(2020); sample(10,3)
trace: sample(10, 3)
[1] 7 6 8
> sample(10,3)
trace: sample(10, 3)
[1] 1 10 4
Hello,
I don't have an answer on the reason why this happens but it seems like
a bug. Where?
In which of `[<-.data.frame` or `[<-.default`?
A solution is to subset and assign the vector:
set.seed(2020)
df2 <- data.frame(unit = 1:10)
df2$treated <- FALSE
df2$treated[sample(nrow(df2), 3)]
> Duncan Murdoch
> on Fri, 19 Jun 2020 10:14:19 -0400 writes:
> On 19/06/2020 9:59 a.m., Jeffrey Dick wrote:
>> Hi Witold,
>>
>> See also this thread on R-pkg-devel. Quoting Duncan Murdoch, "That
>> looks like a bug in grDevices."
> Yes, and the bug is still
Dear all,
any (!) software used in regulated environments has to be validated.
Regrettably is is a misconception by many working in the pharmaceutical
industry that only studies evaluated by SAS are accepted by the FDA.
See this one-pager https://www.fda.gov/media/109552/download and a
I ran into some strange behavior in R when trying to assign a treatment to
rows in a data frame. I'm wondering whether any R experts can explain
what's going on.
First, let's assign a treatment to 3 out of 10 rows as follows.
> df <- data.frame(unit = 1:10)
> df$treated <- FALSE
>
> s <-
Hi
I have a package, which plots from the plantuml syntax (https://plantuml.com)
graphs via a knitr engine, into a file, or into a graphics device
(https://github.com/rkrug/plantuml).
I am using at the moment grImport for the eps import, but would like to cut
down on dependencies.
Is there
On 19/06/2020 9:59 a.m., Jeffrey Dick wrote:
Hi Witold,
See also this thread on R-pkg-devel. Quoting Duncan Murdoch, "That
looks like a bug in grDevices."
Yes, and the bug is still there: grDevices:::.smoothScatterCalcDensity
calls KernSmooth::bkde2D without checking whether KernSmooth is
Hi Witold,
See also this thread on R-pkg-devel. Quoting Duncan Murdoch, "That
looks like a bug in grDevices."
https://stat.ethz.ch/pipermail/r-package-devel/2019q3/004287.html
Cheers,
Jeff
On Wed, Jun 17, 2020 at 4:59 PM Witold E Wolski wrote:
>
> Hello,
>
> I am getting the following error
Thanks, Duncan and Uwe,
I was using Rstudio. This solved the problem
Best Regards
*Ankush Sharma*
On Fri, Jun 19, 2020 at 2:25 PM Duncan Murdoch
wrote:
> On 19/06/2020 8:06 a.m., Ankush Sharma wrote:
> > The packages were installed after the update!
>
> That's not relevant. The issue is
On 19/06/2020 8:06 a.m., Ankush Sharma wrote:
The packages were installed after the update!
That's not relevant. The issue is that the packages were loaded at the
time you tried to update them.
You may have to start R with the --vanilla option to avoid automatically
loading packages if
The packages were installed after the update!
Best Regards
*Ankush Sharma*
On Fri, Jun 19, 2020 at 1:56 PM Uwe Ligges
wrote:
> The packages must not be loaded when you try to update.
>
> Best,
> Uwe Ligges
>
>
>
> On 19.06.2020 12:07, Ankush Sharma wrote:
> > Dear all,
> >
> > I am working R
The packages must not be loaded when you try to update.
Best,
Uwe Ligges
On 19.06.2020 12:07, Ankush Sharma wrote:
Dear all,
I am working R version 4.0.1 macos catalina , I´m not able to load
libraries e.g ggplot2
Error: Error: package or namespace load failed for ‘ggplot2’ in
Dear all,
I am working R version 4.0.1 macos catalina , I´m not able to load
libraries e.g ggplot2
Error: Error: package or namespace load failed for ‘ggplot2’ in
loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘gtable’
Then i tried installing
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