[R] ggtree: color-code multiple paraphyletic clades

I've been using groupOTU to color paraphyletic clades in my tree based on lists of tips, but I have multiple clades I want to highlight. Is there some way to use ggplot to indicate multiple paraphyletic clades? Thank you [[alternative HTML version deleted]]

Re: [R] ggplot2 stat_smooth formula different units

Hello, Try removing I() from I(log(y)). But it's hard to say without a reproducible example, please post the output of dput(dat) or, if dat is big, the output of dput(head(dat, 20)) Hope this helps, Rui Barradas Às 22:11 de 11/11/20, Marcelo Laia escreveu: Hi, I am running these

Re: [R] ggplot2 stat_smooth formula different units

Hi Rui, You are very welcome! On 11/11/20 at 11:10, Rui Barradas wrote: > > dput(head(dat, 20)) > structure(list(Bloco = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), Espacamento = c("3 x 1", "3 x 1", "3 x 1", "3 x 1", "3 x 1", "3 x 1", "3 x 1", "3 x 1",

Re: [R] ggtree: color-code multiple paraphyletic clades

Hello, You should post a reproducible example like the posting guide asks you to. In the mean time, are you looking for [1], section Group Clades, by package ggtree author? It even seems to be the package vignette. [1]

Re: [R] ggtree: color-code multiple paraphyletic clades

Thank you, it seems the solution is to define the nodes in groupOTU using a list of vectors. On Thu, Nov 12, 2020 at 12:15 PM Rui Barradas wrote: > Hello, > > You should post a reproducible example like the posting guide asks you to. > In the mean time, are you looking for [1], section Group

Re: [R] R ioanalysis pkg

Thank you very much Bert and David, I appreciate your kind answers which will be of great help to me no doubt. G On Tue, Nov 10, 2020 at 7:08 PM Bert Gunter wrote: > There are around 20,000 specialized packages for R. This list is set up to > help on standard R features and packages, but

Re: [R] [effects] Wrong xlevels in effects plot for mixed effects model when multiline = TRUE

Dear Gerrit, The bug you reported should now be fixed in the development version 4.2-1 of the effects package, which you can currently install from R-Forge via install.packages("effects", repos="http://R-Forge.R-project.org;) . Eventually, the updated version of the effects package will be

[R] please help with "could not find function "ComBat.mc" "

Hi All, I am very sorry to bother you. This week, I updated my R from 3.5.3  to 4.0.3, reinstalled all required R packages and reran the following R code; then got the following error: could not find function "ComBat.mc". > #' firstly Removing chip-well batch effects using ComBat from the

[R] ggplot2 stat_smooth formula different units

Hi, I am running these approaches: Model 1 ggplot( dat , aes(x=DAP, y=Altura, color=as.factor(Espacamento) )) + geom_point(size=0.5) + stat_smooth(method = "lm", formula = y ~ x + I(x^2), size = 1) + facet_grid(Espacamento ~ Clone) +

Re: [R] analyzing results from Tuesday's US elections

Please watch this video if you wrongly believe that Benford's law easily can be applied to elections results. https://youtu.be/etx0k1nLn78 On Sun, Nov 1, 2020, 21:17 Spencer Graves < spencer.gra...@effectivedefense.org> wrote: > Hello: > > >What can you tell me about plans to analyze

Re: [R] please help with "could not find function "ComBat.mc" "

Hi Yuan, The package named "Enmix" is maintained on Bioconductor. It seems to be specific to particular lab equipment and so all I can advise is: 1) Try your question on the Bioconductor help list 2) If no help there contact Zongli Xu (the maintainer) Jim On Thu, Nov 12, 2020 at 11:40 AM Yuan

Re: [R] ggplot2 stat_smooth formula different units

On 11/11/20 2:11 PM, Marcelo Laia wrote: Hi, I am running these approaches: Model 1 ggplot( dat , aes(x=DAP, y=Altura, color=as.factor(Espacamento) )) + geom_point(size=0.5) + stat_smooth(method = "lm", formula = y ~ x + I(x^2), size = 1) +

Re: [R] Error Message With the "MCMCmixfactanal" Function

Please read and follow the posting guide linked below, especially this: "For questions about functions in standard packages distributed with R (see the FAQ Add-on packages in R ), ask questions on R-help. If the question relates

[R] Error Message With the "MCMCmixfactanal" Function

To Whom It May Concern, In am using the script below to test the function "MAMCmixfactanal" in the package "MCMCpack". library(MCMCpack) data(PErisk) post <- MCMCmixfactanal(~courts+barb2+prsexp2+prscorr2+gdpw2, factors=1, data=PErisk, lambda.constraints=

[R] Data transformation problem

I am stuck on a data transformation problem. I have a data frame, df1 in my example, with some original "levels" data. The data pertain to some variable, such as GDP, in various reference periods, REF, as estimated and released in various release periods, REL. The release periods follow after

Re: [R] Data transformation problem

I am not a data.table afficiando, but here is how I would do it with dplyr/tidyr: library(dplyr) library(tidyr) do_per_REL <- function( DF ) { rng <- range( DF$REF1 ) # watch out for missing months? DF <- ( data.frame( REF1 = seq( rng[ 1 ], rng[ 2 ], by = "month" ) ) %>%

Re: [R] Error Message With the "MCMCmixfactanal" Function

Someone may feel like tackling this anyway, but technically it is off-topic here, as this forum is about the R language rather than specific contributed packages. (http://www.r-project.org/posting-guide.html). Lookup the package DESCRIPTION file on CRAN and if it does not mention a recommended