[R] Violin plot with mean_sdl

Hi, I followed the example described at [1] but I don't know why I get the following warning > library(ggplot2) > library(Hmisc) > mydata <- read.csv('test.csv', header=T,row.names=1) > mydata V1 V2 V3 V4 P1 73.6 0.7 74.6 R P2 75.2 0.7 75.8 R P3 6.5 0.0 7.3 R P4 41.4 0.3 39.2 C P5

Re: [R] Controling the presentation of violin plot

>Alternatively, plot the y axis in a log scale. Since there are zeros in >the data, scales::pseudo_log_trans, will be used. > >p + geom_dotplot(binaxis='y', stackdir='center', dotsize=1) + > scale_y_continuous( > trans = scales::pseudo_log_trans(base = exp(1)) > ) Yes that is a good hint

Re: [R] Controling the presentation of violin plot

Hello, If the problem is the dots sizes, why not reduce it? Below I have dotsize=0.5, half of yours. p + geom_dotplot(binaxis='y', stackdir='center', dotsize=0.5) Alternatively, plot the y axis in a log scale. Since there are zeros in the data, scales::pseudo_log_trans, will be used. p + g

Re: [R] Controling the presentation of violin plot

Hi Mahmood, As I don't know what "mydata" is, I'll have to fake it. Do you want something like this? yourdata<-data.frame(x1=c(1250,600,rep(200,9)), x2=c(7000,2300,800,rep(100,8)), x3=c(8900,950,300,rep(0,8)), x4=c(1400,1000,rep(600,4),rep(200,5))) library(plotrix) violin_plot(yourdata) Jim O

Re: [R] using MAP and PURR to compute characteristic roots

Since purrr:map() is functionally identical to lapply, it is not at all clear to me what you are having trouble with. What output did you want? On March 31, 2021 5:10:29 PM PDT, Veerappa Chetty wrote: >I have to compute characteristic roots for 100s of U.S.counties. I got >help using " lapply".

Re: [R] using MAP and PURR to compute characteristic roots

On 3/31/21 5:10 PM, Veerappa Chetty wrote: I have to compute characteristic roots for 100s of U.S.counties. I got help using " lapply". I prefer using MAP and PURR if that is possible. I am using them to compute linear regressions. Here is my test problem and the output. I would appreciate any

[R] using MAP and PURR to compute characteristic roots

I have to compute characteristic roots for 100s of U.S.counties. I got help using " lapply". I prefer using MAP and PURR if that is possible. I am using them to compute linear regressions. Here is my test problem and the output. I would appreciate any help. Thanks V.K.Chetty test.dat<- tibble

Re: [R] FD package_dbFD error

Hi, While Bert is right that this would be a good question for r-sig-ecology, I think you might have made a very simple-to-fix mistake: According to https://www.rdocumentation.org/packages/FD/versions/1.0-12/topics/dbFD if you don't name the arguments, traits should come BEFORE sites. If that d

[R] Controling the presentation of violin plot

Hi, With the following command, I get a messy violin plot which can be seen at https://pasteboard.co/JVdZKNz.jpg p <- ggplot(mydata, aes(x=BE, y=INT)) + geom_violin(trim=FALSE) p + geom_dotplot(binaxis='y', stackdir='center', dotsize=1) It seems that the y-axis has a large scale and that caus

Re: [R] FD package_dbFD error

I think you would more likely find the help you seek on the r-sig-ecology list rather than here. Also, do note per the posting guide linked below: "For questions about functions in standard packages distributed with R (see the FAQ Add-on packages in R

[R] FD package_dbFD error

Hi everyone, I am trying to conduct dbFD from the FD package, but it keeps giving me the same error: ex1 <- dbFD(sites, traits) Error in dbFD(sites, traits) : Different number of species in 'x' and 'a'. Ab, bb, Ci are species names. I have tried rewriting the species names so many times

[R] how to quantify outliers on multi-dimensional scaling plot?

Hello, I am in process of writing a grant where I am explaining my planned methylation analysis using R software "minfi". In the text of the grant I am mentioning looking for samples containing outliers in the multi-dimensional scaling (MDS) plot https://rdrr.io/bioc/minfi/man/mdsPlot.html . My qu

Re: [R] cox.zph

Yes. :-) Best regards -- Gerrit - Dr. Gerrit Eichner Mathematical Institute, Room 212 gerrit.eich...@math.uni-giessen.de Justus-Liebig-University Giessen Tel: +49-(0)641-99-32104 Arndtstr. 2, 3539

[R] cox.zph

Colleagues, I would like to make certain that my understanding of the tabular output produced by cox.zph is correct. Am I correct that the NULL hypothesis being tested is that the hazard is proportional in time? Therefor a non-significant result indicates that we don't have evidence that the

Re: [R] [EXT] Calculating the total change in shareprice over a time periond

Mr. Blueyonder, There are a number of problems with this. 1) is the data below really in a data frame? I coerced your table into a data frame, guessing at the structure and when I print out the 1st three rows I get an alignment into proper columns COMPANY_NUMBER COMPANY_NAME    C

[R] Calculating the total change in shareprice over a time periond

Dear All, I have a data frame which is structured as follows: COMPANY_NUMBER COMPANY_NAMECITYYEAR_END_DATE CLOSE_SHARE_PRICE 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham 30/09/2005 NA 22705 CARDIFF PROPERTY PUBLIC LIMITED COMPANY (THE)Egham

[R] [Rd] R 4.0.5 is released

The build system rolled up R-4.0.5.tar.gz (codename "Shake and Throw") this morning. This is a very minor update, mostly to fix the annoyance with East Asian character sets. The list below details the changes in this release. You can get the source code from https://cran.r-project.org/src/ba

Re: [R] Working with violin plot

Yes thank you very much. Regards, Mahmood From: Eric Berger Sent: Wednesday, March 31, 2021 11:30:48 AM To: Mahmood Naderan-Tahan Cc: r-help@r-project.org Subject: Re: [R] Working with violin plot Try replacing ggplot(ToothGrowth, ... ) with ggplot(mydata,...)

Re: [R] Working with violin plot

Try replacing ggplot(ToothGrowth, ... ) with ggplot(mydata,...) HTH, Eric On Wed, Mar 31, 2021 at 12:20 PM Mahmood Naderan-Tahan < mahmood.nade...@ugent.be> wrote: > Hi > > I would like to use the violin plot as described in the manual [1]. In the > example, I see > > ToothGrowth$dose <- as.fac

Re: [R] Working with violin plot

Please ignore the previous email... Regards, Mahmood From: R-help on behalf of Mahmood Naderan-Tahan Sent: Wednesday, March 31, 2021 11:19:59 AM To: r-help@r-project.org Subject: [R] Working with violin plot Hi I would like to use the violin plot as describe

[R] Working with violin plot

Hi I would like to use the violin plot as described in the manual [1]. In the example, I see ToothGrowth$dose <- as.factor(ToothGrowth$dose) head(ToothGrowth) On the other hand, my data is a csv file containing some rows and numbers. Problem is that the following code doesn't work > mydata <