Re: [R] PLOTTING ODE MODEL RESULTS USING PLOT.DESOLVE FROM THE DESOLVE PACKAGE

2025-03-25 Thread Jeff Newmiller via R-help
a) Do be sure to read the Posting Guide... for example changes to contributed packages is appropriate for communicating directly to the maintainer or via the recommended forum for that contributed package. Also, you will avoid mis-communication more reliably if you follow the guide recommendatio

Re: [R] plotting nnet function....

2024-07-27 Thread Ivan Krylov via R-help
В Sat, 27 Jul 2024 11:00:34 + akshay kulkarni пишет: > My question is : how to plot the final model on the actual data > points? Have you been able to obtain the predictions? What happens if you call predict() on the model object returned to you by train()? Once you have both the data and t

Re: [R] Plotting Fitted vs Observed Values in Logistic Regression Model

2023-08-02 Thread Rui Barradas
Às 14:57 de 01/08/2023, Paul Bernal escreveu: Dear friends, I hope this email finds you all well. This is the dataset I am working with: dput(random_mod12_data2) structure(list(Index = c(1L, 5L, 11L, 3L, 2L, 8L, 9L, 4L), x = c(5, 13, 25, 9, 7, 19, 21, 11), n = c(500, 500, 500, 500, 500, 500, 50

Re: [R] Plotting Fitted vs Observed Values in Logistic Regression Model

2023-08-01 Thread Ben Bolker
logistic_regmod2 <- glm(formula = ratio~x, family = binomial(logit), data = random_mod12_data2, weights =n) plot(ratio ~ x, data = random_mod12_data2) pframe <- data.frame(x = sort(random_mod12_data2$x)) pframe$ratio <- predict(logistic_regmod2, newdata = pframe, type = "response") with(pframe

Re: [R] Plotting factors in graph panel

2023-07-11 Thread Anupam Tyagi
a.cz/en/personal-data-protection-principles/ >> > <https://www.precheza.cz/en/personal-data-protection-principles/>* >> > >> > *Důvěrnost: *Tento e-mail a jakékoliv k němu připojené dokumenty jsou >> > důvěrné a podléhají tomuto právně závaznému prohlášení

Re: [R] Plotting factors in graph panel

2023-07-11 Thread Deepayan Sarkar
jakékoliv k němu připojené dokumenty jsou > > důvěrné a podléhají tomuto právně závaznému prohlášení o vyloučení > > odpovědnosti: *https://www.precheza.cz/01-dovetek/ > > <https://www.precheza.cz/01-dovetek/>* | This email and any documents > > attached to it may b

Re: [R] Plotting factors in graph panel

2023-07-11 Thread Anupam Tyagi
hed to it may be confidential and are subject to the legally binding > disclaimer: *https://www.precheza.cz/en/01-disclaimer/ > <https://www.precheza.cz/en/01-disclaimer/>* > > > > *From:* Anupam Tyagi > *Sent:* Friday, July 7, 2023 12:48 PM > *To:* PIKAL Petr > *Cc:*

Re: [R] Plotting factors in graph panel

2023-07-07 Thread PIKAL Petr
M To: PIKAL Petr Cc: r-help@r-project.org Subject: Re: [R] Plotting factors in graph panel Thanks! You are correct, the graphs look very similar, except ggplot is scaling the text font to make it more readable. Is there a way to scale down the x-axis labels, so they are readable?

Re: [R] Plotting factors in graph panel

2023-07-07 Thread Anupam Tyagi
; From: R-help On Behalf Of Deepayan Sarkar > > Sent: Thursday, July 6, 2023 3:06 PM > > To: Anupam Tyagi > > Cc: r-help@r-project.org > > Subject: Re: [R] Plotting factors in graph panel > > > > On Thu, 6 Jul 2023 at 15:21, Anupam Tyagi wrote: > > > &

Re: [R] Plotting factors in graph panel

2023-07-07 Thread Anupam Tyagi
ot;, "Bank Current 2", "Bank Current 2", > > > "Bank Current 2", "Bank Current 2", "Bank Savings 2", "Bank Savings 2", > > > "Bank Savings 2", "Bank Savings 2", "Bank Savings 2", "MF None 3

Re: [R] Plotting factors in graph panel

2023-07-06 Thread PIKAL Petr
ent: Thursday, July 6, 2023 3:06 PM > To: Anupam Tyagi > Cc: r-help@r-project.org > Subject: Re: [R] Plotting factors in graph panel > > On Thu, 6 Jul 2023 at 15:21, Anupam Tyagi wrote: > > > > Btw, I think "lattice" graphics will provide a better solution than

Re: [R] Plotting factors in graph panel

2023-07-06 Thread Deepayan Sarkar
ank None 2", "Bank Current 2", "Bank Current 2", "Bank Current 2", > > "Bank Current 2", "Bank Current 2", "Bank Savings 2", "Bank Savings 2", > > "Bank Savings 2", "Bank Savings 2", "

Re: [R] Plotting factors in graph panel

2023-07-06 Thread Anupam Tyagi
ot;Bank Savings 2", "Bank Savings 2", "MF None 3", > "MF None 3", "MF None 3", "MF None 3", "MF None 3", "MF Equity 3", > "MF Equity 3", "MF Equity 3", "MF Equity 3", "MF Equity 3", "MF

Re: [R] Plotting factors in graph panel

2023-07-06 Thread Anupam Tyagi
None 3", "MF None 3", "MF None 3", "MF None 3", "MF None 3", "MF Equity 3", "MF Equity 3", "MF Equity 3", "MF Equity 3", "MF Equity 3", "MF Debt 3", "MF Debt 3", "MF Debt 3&q

Re: [R] Plotting factors in graph panel

2023-07-05 Thread Anupam Tyagi
I am working with Jim's solution, but I am getting some errors. I organized the data in Excel and read into R using the Import option in the menu of R-Studio. For some reason it is telling me my data is a Tibble and not a dataframe. Am I using Tidyverse unknowingly? I thought I was working in base-

Re: [R] Plotting factors in graph panel

2023-07-03 Thread PIKAL Petr
Behalf Of Anupam Tyagi > Sent: Monday, July 3, 2023 11:54 AM > To: Jim Lemon > Cc: r-help mailing list > Subject: Re: [R] Plotting factors in graph panel > > Attached is another example plot, that is better than the earlier one. > > On Mon, 3 Jul 2023 at 15:21, Anupam Tya

Re: [R] Plotting factors in graph panel

2023-07-03 Thread Anupam Tyagi
Attached is another example plot, that is better than the earlier one. On Mon, 3 Jul 2023 at 15:21, Anupam Tyagi wrote: > I thought maybe I can share with you how the data looks in Excel, and an > example plot I found on the web that looks similar to what I want to plot. > These are attached to

Re: [R] Plotting factors in graph panel

2023-07-03 Thread Anupam Tyagi
Thanks Jim, thanks everyone. I was caught up with work and moving home, so a delay in response. I tried running the code you provided and it is not running well in my R-Studio setup. It is giving errors and not producing plots. I don't yet understand all the code well yet, so I need to work on it a

Re: [R] Plotting factors in graph panel

2023-06-29 Thread Jim Lemon
Okay. Here is a modification that does four single line plots. at_df<-read.table(text= "Income MF MF_None MF_Equity MF_Debt MF_Hybrid Bank_None Bank_Current Bank_Savings Bank_NA $10 1 3.05 29.76 31.18 36.0 46.54 24.75 25.4 3.307 $25 2 2.29 28.79 32.64 36.27 54.01 24.4 18.7 2.891 $40 3 2.24 29.

Re: [R] Plotting factors in graph panel

2023-06-29 Thread John Kane
w > $10 do not make much sense compared to other values. > > I am tired of guessing. > > Tim > > -Original Message- > From: R-help On Behalf Of Anupam Tyagi > Sent: Wednesday, June 28, 2023 11:49 PM > To: r-help@r-project.org > Subject: Re: [R] Plotting f

Re: [R] Plotting factors in graph panel

2023-06-29 Thread Ebert,Timothy Aaron
. The values below $10 do not make much sense compared to other values. I am tired of guessing. Tim -----Original Message- From: R-help On Behalf Of Anupam Tyagi Sent: Wednesday, June 28, 2023 11:49 PM To: r-help@r-project.org Subject: Re: [R] Plotting factors in graph panel [External Email

Re: [R] Plotting factors in graph panel

2023-06-28 Thread PIKAL Petr
ts variable names to fit your needs. Cheers Petr > -Original Message- > From: R-help On Behalf Of Anupam Tyagi > Sent: Thursday, June 29, 2023 5:49 AM > To: r-help@r-project.org > Subject: Re: [R] Plotting factors in graph panel > > Thanks, Pikal and Jim. Yes, it has

Re: [R] Plotting factors in graph panel

2023-06-28 Thread Anupam Tyagi
Thanks, Pikal and Jim. Yes, it has been a long time Jim. I hope you have been well. Pikal, thanks. Your solution may be close to what I want. I did not know that I was posting in HTML. I just copied the data from Excel and posted in the email in Gmail. The data is still in Excel, because I have no

Re: [R] Plotting factors in graph panel

2023-06-28 Thread Jim Lemon
Hi Anupam, Haven't heard from you in a long time. Perhaps you want something like this: at_df<-read.table(text= "Income MF MF_None MF_Equity MF_Debt MF_Hybrid Bank_None Bank_Current Bank_Savings Bank_NA $10 1 3.05 29.76 31.18 36.0 46.54 24.75 25.4 3.307 $25 2 2.29 28.79 32.64 36.27 54.01 24.4 1

Re: [R] Plotting factors in graph panel

2023-06-28 Thread PIKAL Petr
Hi You probably can use any package including base R for such plots. 1. Posting in HTML scrambles your date so they are barely readable. 2. Use dput(head(yourdata, 20)) and copy the output to your mail to show how your data look like. Although it seems to be not readable, R will consumes it freel

Re: [R] Plotting directly to memory?

2023-05-28 Thread Jan van der Laan
Perhaps the ragg package? That has an `agg_capture` device "that lets you access the device buffer directly from your R session." https://github.com/r-lib/ragg HTH, Jan On 28-05-2023 13:46, Duncan Murdoch wrote: Is there a way to open a graphics device that plots entirely to an array or

Re: [R] Plotting directly to memory?

2023-05-28 Thread Jeroen Ooms
On Sun, May 28, 2023 at 1:46 PM Duncan Murdoch wrote: > > Is there a way to open a graphics device that plots entirely to an array > or raster in memory? I'd prefer it to use base graphics, but grid would > be fine if it makes a difference. > > For an explicit example, I'd like to do the equivale

Re: [R] Plotting a triangular prism

2022-11-11 Thread Ebert,Timothy Aaron
Hi Erin, Note that the HTML version was deleted in RHelp. Whatever was there was not seen by anyone else. Not sure this is what you want, but try "mixture designs in R" as a google search. There are a number of options therein. Regards, Tim -Original Message- From: R-help On Beh

Re: [R] Plotting a triangular prism

2022-11-11 Thread Erin Hodgess
Great, thank you! Sincerely, Erin On Thu, Nov 10, 2022 at 11:56 PM Jim Lemon wrote: > Hi Erin, > If you want a realistic 3D prism, I would use something like POVRay or > other rendering software. You have to know your geometry, but you can > get a very realistic image. I suspect that you want m

Re: [R] Plotting a triangular prism

2022-11-10 Thread Jim Lemon
Hi Erin, If you want a realistic 3D prism, I would use something like POVRay or other rendering software. You have to know your geometry, but you can get a very realistic image. I suspect that you want more than just a picture of a prism, so you can then generate a PNG image and use it as a layer i

Re: [R] Plotting a triangular prism

2022-11-10 Thread David Winsemius
One might think that after all these years you would have understood that “it’s not working” is an excessively imprecise description of, well, anything. Also html is deprecated severely on Rhelp. — David. Sent from my iPhone > On Nov 10, 2022, at 5:46 PM, Erin Hodgess wrote: > > Hello!

Re: [R] Plotting proportions

2022-04-03 Thread Jim Lemon
Hi Nick, If you can bear using R base graphics, the plotrix package has a function named "getYmult" that allows you to adjust for the aspect ratio of any plot area. Jim On Sun, Apr 3, 2022 at 11:14 PM Nick Wray wrote: > > Hello If you plot a square in the default R studio window you see a > rec

Re: [R] Plotting proportions

2022-04-03 Thread Bert Gunter
... and following up on Rui's reply, assuming that the default (in R, not RStudio) "m" is being used, I would assume that the aspect ratio in the RStudio device depends on the layout of your windows. Also, you might do better asking here, https://community.rstudio.com/ , than on this list. Bert Gu

Re: [R] Plotting proportions

2022-04-03 Thread Rui Barradas
Hello, There's a graphics parameter for aspect ratio that you can set asp=1 on a plot by plot basis. But you also need to change pty. From ?par: pty A character specifying the type of plot region to be used; "s" generates a square plotting region and "m" generates the maximal plotting region.

Re: [R] plotting some rows in different color

2021-09-02 Thread Jim Lemon
Hi Eliza This seems to work: plot(BFA3[,1],BFA3[,4], pch=16, xlab = "", ylab = "",col=(BFA3[,2]==BFA3[,3])+2,axes=FALSE) but I have no idea what you are trying to do with the as.numeric(as.Date(...)) business. Jim On Fri, Sep 3, 2021 at 8:44 AM Eliza Botto wrote: > > Dear useRs, > > For the

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-08-02 Thread Rolf Turner
On Mon, 2 Aug 2021 17:53:34 +0100 Rui Barradas wrote: > Hello, > > I'm glad it helped. > Here are a couple of ideas for theme. Thanks Rui. The scope of your knowledge and understanding is simply amazing! cheers, Rolf -- Honorary Research Fellow Department of Statistics University of Au

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-08-02 Thread Rui Barradas
Hello, I'm glad it helped. Here are a couple of ideas for theme. 1) From ?theme: Theme inheritance Theme elements inherit properties from other theme elements hierarchically. For example, axis.title.x.bottom inherits from axis.title.x which inherits from axis.title, which in turn inherits fro

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-08-02 Thread Rolf Turner
I would like to tie off this thread (?!?!) by thanking Jeff Newmiller, Rui Barradas, Avi Gross and Bill Dunlap for their advice and insight. I have attached the code that I finally put together, on the basis of the aforementioned advice, in the file ciPlot.txt. I have also attached the necessary

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-07-20 Thread Rolf Turner
Thanks to Bill Dunlap and Avi Gross for their clear and helpful answers to my questions. cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-help@r-project.org mailin

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-07-19 Thread Avi Gross via R-help
Of Rolf Turner Sent: Monday, July 19, 2021 7:24 PM To: r-help@r-project.org Subject: Re: [R] Plotting confidence intervals with ggplot, in multiple facets. Thanks to Jeff Newmiller, Rui Barradas and Avi Gross for their extremely helpful replies. I have got both Jeff's and Rui&#

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-07-19 Thread Bill Dunlap
ggplot2::labs() interprets expressions as plotmath. E.g., data.frame(X=1:10,Y=(1:10)^2) %>% ggplot(aes(X,Y)) + geom_point() + labs(x = expression(beta), y = expression(beta^2)) -Bill On Mon, Jul 19, 2021 at 4:24 PM Rolf Turner wrote: > > > Thanks to Jeff Newmiller, Rui Barradas and

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-07-19 Thread Rolf Turner
Thanks to Jeff Newmiller, Rui Barradas and Avi Gross for their extremely helpful replies. I have got both Jeff's and Rui's code to run. I am currently experimenting with Avi's suggestion of producing multiple plots and then putting them together using plotgrid() or grid.arrange(). This idea s

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-07-18 Thread Avi Gross via R-help
Rolf, Your example shows two plots with one above the other. If that is what you want, then a solution like the one Jeff provided using facet_grid() to separate data based on the parameter value. It also scales up if you add additional sets of data for gamma and delta up to a point. An alterna

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-07-18 Thread Rui Barradas
Hello, Something like this? library(ggplot2) eg <- dget("data/egData.txt") ggplot(eg, aes(Ndat, estimate)) + � geom_errorbar(aes(ymin = lower, ymax = upper), width = 20) + � geom_point(colour = "slateblue", size = 1) + � geom_hline(yintercept = 0, colour = "red") + � facet_grid(param ~ .) +

Re: [R] Plotting confidence intervals with ggplot, in multiple facets.

2021-07-17 Thread Jeff Newmiller
ggplot(dta,aes(x=Ndat,y=estimate, ymin=lower,ymax=upper))+ geom_point() + geom_errorbar(width=30) + facet_grid(param~1) + theme_minimal() Width parameter seems odd... play with it I suppose. For facets, you can also use facet_wrap(~param, ncol=1). ggplot is very much about the data and t

Re: [R] Plotting the ASCII character set.

2021-07-07 Thread Rolf Turner
Thanks to Ivan Krylov, David Winsemius and Duncan Murdoch for their informative replies to my cri de coeur. The most complete answer was however provided off-list by Andrew Simmons who wrote a new and carefully structured function plotASCII() to replace my old no-longer functioning plot_ascii() f

Re: [R] Plotting the ASCII character set.

2021-07-04 Thread Duncan Murdoch
On 03/07/2021 9:59 p.m., Rolf Turner wrote: ... deletia ... Also note that there is a bit of difference between the results of using Encoding() and the results of using iconv(). E.g. if I do a <- "\x80" b <- iconv(a,"latin1","UTF-8") Encoding(a) <- "latin1" then when I type "a" I get the Eur

Re: [R] Plotting the ASCII character set.

2021-07-04 Thread Ivan Krylov
On Sun, 4 Jul 2021 13:59:49 +1200 Rolf Turner wrote: > a substantial number of the characters are displayed as a wee > rectangle containing a 2 x 2 array of digits such as > > > 0 0 > > 8 0 Interesting. I didn't pay attention to it at first, but now I see that a range of code points, U+00

Re: [R] Plotting the ASCII character set.

2021-07-03 Thread David Winsemius
Sent from my iPhone > On Jul 3, 2021, at 7:00 PM, Rolf Turner wrote: > >  >> On Sat, 3 Jul 2021 09:40:28 +0200 >> Ivan Krylov wrote: >> >> Hello Rolf Turner, >> >> On Sat, 3 Jul 2021 14:02:59 +1200 >> Rolf Turner wrote: >> >>> Can anyone suggest how I might get my plot_ascii() function

Re: [R] Plotting the ASCII character set.

2021-07-03 Thread Rolf Turner
On Sat, 3 Jul 2021 09:40:28 +0200 Ivan Krylov wrote: > Hello Rolf Turner, > > On Sat, 3 Jul 2021 14:02:59 +1200 > Rolf Turner wrote: > > > Can anyone suggest how I might get my plot_ascii() function working > > again? Basically, it seems to me, the question is: how do I > > persuade R to r

Re: [R] Plotting the ASCII character set.

2021-07-03 Thread Ivan Krylov
Hello Rolf Turner, On Sat, 3 Jul 2021 14:02:59 +1200 Rolf Turner wrote: > Can anyone suggest how I might get my plot_ascii() function working > again? Basically, it seems to me, the question is: how do I persuade > R to read in "\260" as "\ub0" rather than "\xb0"? Part of the problem is that

Re: [R] Plotting Coxph model with an interaction.

2021-05-20 Thread Gerrit Eichner
Hi, John, it should work the same way as without interaction (but make sure to use the fitted object "coxfit", not just "fit" in our call of survfit, and note that age*rx already expands to age + rx + age:rx so that age + rx is redundant in your formula): coxfit <- coxph(Surv(futime, fustat) ~ a

Re: [R] Plotting Coxph model with an interaction.

2021-05-20 Thread Bert Gunter
Perhaps this might be useful: https://rpubs.com/tf_peterson/interactionplotDemo 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 Thu, May 20, 2021 at 10:29 AM S

Re: [R] Plotting two time series in one graph

2021-05-02 Thread Rui Barradas
Hello, Can you post sample data? For instance, the output of dput(head(dovrez, 20)) dput(head(rqa_df_USD, 20)) Or maybe you could rbind the data.frames with one column telling which of Res or LAM the values come from. Hope this helps, Rui Barradas Às 19:38 de 02/05/21, Baki UNAL via R-he

Re: [R] Plotting adjusted KM curve

2021-04-09 Thread Göran Broström
On 2021-04-05 03:34, Sorkin, John wrote: Colleagues, I am using the coxph to model survival time. How do I plot an adjusted Kaplan Meir plot resulting from coxph? The code I would like to run would start with: # run cox model fit1Cox <- coxph(surv_object ~age+sex,data=mydata) I have no idea

Re: [R] Plotting adjusted KM curve

2021-04-09 Thread PIKAL Petr
Hi Google answered https://rdrr.io/bioc/survcomp/man/km.coxph.plot.html Is it what do you want? Cheers Petr > -Original Message- > From: R-help On Behalf Of Sorkin, John > Sent: Monday, April 5, 2021 3:35 AM > To: r-help@r-project.org (r-help@r-project.org) > Subject: [R] Plotting ad

Re: [R] Plotting adjusted KM curve

2021-04-04 Thread John Fox
On 2021-04-04 10:45 p.m., John Fox wrote: Dear John, I think that what you're looking for is plot(survfit(fit1Cox, newdata=data.frame(age=rep(65, 2), sex=factor("female", "male" Whoops, that should be plot(survfit(fit1Cox, newdata=data.frame(age=rep(65, 2), sex=factor(c("female", "male

Re: [R] Plotting adjusted KM curve

2021-04-04 Thread John Fox
Dear John, I think that what you're looking for is plot(survfit(fit1Cox, newdata=data.frame(age=rep(65, 2), sex=factor("female", "male" assuming, of course, that sex is a factor with levels "female" and "male". I hope this helps, John John Fox, Professor Emeritus McMaster University Ha

Re: [R] Plotting world maps with locations.

2021-02-13 Thread Romanus Ejike
Awesome, thanks! I will make corrections and see if it will work. On Sat, Feb 13, 2021 at 6:04 AM David Winsemius wrote: > > > Sent from my iPhone > > > On Feb 12, 2021, at 9:01 PM, David Winsemius > wrote: > > > >  > > > > Sent from my iPhone > > > >> On Feb 12, 2021, at 1:35 PM, Jibrin Alhas

Re: [R] Plotting world maps with locations.

2021-02-12 Thread David Winsemius
Sent from my iPhone > On Feb 12, 2021, at 9:01 PM, David Winsemius wrote: > >  > > Sent from my iPhone > >> On Feb 12, 2021, at 1:35 PM, Jibrin Alhassan >> wrote: >> >> Hello Romanus, >> You are to post only the code and the error messages and not all the >> information from your termi

Re: [R] Plotting world maps with locations.

2021-02-12 Thread David Winsemius
Sent from my iPhone > On Feb 12, 2021, at 1:35 PM, Jibrin Alhassan > wrote: > > Hello Romanus, > You are to post only the code and the error messages and not all the > information from your terminal in R session. That’s not actually the best practice for rhelp questions. More info is bette

Re: [R] Plotting world maps with locations.

2021-02-12 Thread Jibrin Alhassan
Hello Romanus, You are to post only the code and the error messages and not all the information from your terminal in R session. On Fri, Feb 12, 2021, 4:35 PM Romanus Ejike wrote: > Please, I need help from anyone that can solve this problem. > I wanted to plot a world map with locations and nam

Re: [R] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R

2020-02-07 Thread pooja sinha
Thanks, I'll check it out. On Fri, Feb 7, 2020 at 1:08 PM Martin Morgan wrote: > Probably have more success asking on https://support.bioconductor.org. > > Martin Morgan > > On 2/7/20, 12:57 PM, "R-help on behalf of pooja sinha" < > r-help-boun...@r-project.org on behalf of pjsinh...@gmail.com>

Re: [R] Plotting DMRs (Differentially Methylated Regions) using Gviz package in R

2020-02-07 Thread Martin Morgan
Probably have more success asking on https://support.bioconductor.org. Martin Morgan On 2/7/20, 12:57 PM, "R-help on behalf of pooja sinha" wrote: Hi All, I have a file list consisting of Chromosome, Start , End & Methylation Difference in the following format in excel:

Re: [R] Plotting confidence intervals

2019-12-08 Thread phil
Thanks so much Jim. Yes, this is giving me what I want. Philip On 2019-12-08 05:00, Jim Lemon wrote: Hi Philip, This may be a starter: attach(airquality) heights <- tapply(Temp,Month,mean) temp_sd<-tapply(Temp,Month,sd) lower <- tapply(Temp,Month,function(v) t.test(v)$conf.int[1]) upper <- tap

Re: [R] Plotting confidence intervals

2019-12-08 Thread Jim Lemon
Hi Philip, This may be a starter: attach(airquality) heights <- tapply(Temp,Month,mean) temp_sd<-tapply(Temp,Month,sd) lower <- tapply(Temp,Month,function(v) t.test(v)$conf.int[1]) upper <- tapply(Temp,Month,function(v) t.test(v)$conf.int[2]) library(plotrix) barp(heights,ylim=c(0,100),names.arg=m

Re: [R] Plotting confidence intervals

2019-12-08 Thread phil
Thanks for these helpful suggestions. These options don't work in my case because I don't know the individual observations (the dots). A statistical agency collects the observations and keeps them confidential. It provides the mean value and the standard deviation, plus the fact that the obser

Re: [R] Plotting confidence intervals

2019-12-07 Thread Ben Tupper
Hi, Would something like yarrr do the trick? https://ndphillips.github.io/yarrr.html Or gghalves? https://github.com/erocoar/gghalves Cheers, Ben On Sat, Dec 7, 2019 at 9:32 PM wrote: > I want to show little bell curves on my bar chart to illustrate the > confidence ranges. The following ex

Re: [R] Plotting hclust() results

2019-08-06 Thread Rui Barradas
Hello, I don't know if you want something like this: hc_long <- reshape::melt(hc, id.vars = "Cluster") # convert to long format library(ggplot2) ggplot(hc_long, aes(x = Cluster, y = value, colour = variable)) + geom_point() + geom_line() + coord_flip() + facet_wrap(~ variable) #Data

Re: [R] Plotting in R

2019-07-18 Thread nstefi
Steven -Original Message- From: Jim Lemon Sent: Thursday, July 18, 2019 5:25 AM To: nst...@gmail.com Cc: r-help mailing list Subject: Re: [R] Plotting in R Hi Steven, I caved in and installed plotly. Not an easy task. When I tried your example, I got a blank HTML page displayed. I the

Re: [R] Plotting in R

2019-07-18 Thread Jim Lemon
gt; tickmode = "array", > tickangle = 270 > )) > > Any ideas? > > Thanks, > Steven > > -Original Message- > From: nst...@gmail.com > Sent: Tuesday, July 16, 2019 9:55 AM > To: 'Jim Lemon' > Cc: 'r-help mailing l

Re: [R] Plotting in R

2019-07-16 Thread nstefi
Sent: Tuesday, July 16, 2019 9:55 AM To: 'Jim Lemon' Cc: 'r-help mailing list' Subject: RE: [R] Plotting in R OK, I think I got this: For example every 3rd element would be: sydf$monthday[seq(1, length(sydf$monthday), 3)] Thanks, Steven -Original Message- From: nst..

Re: [R] Plotting in R

2019-07-16 Thread nstefi
OK, I think I got this: For example every 3rd element would be: sydf$monthday[seq(1, length(sydf$monthday), 3)] Thanks, Steven -Original Message- From: nst...@gmail.com Sent: Tuesday, July 16, 2019 9:39 AM To: 'Jim Lemon' Cc: 'r-help mailing list' Subject: R

Re: [R] Plotting in R

2019-07-16 Thread nstefi
: Friday, July 12, 2019 6:41 PM To: nst...@gmail.com Cc: r-help mailing list Subject: Re: [R] Plotting in R Oh, sorry, I think I see what you have tried to do. You want yearly ticks but month-day labels. These won't mean much unless you also have the year. If you ask for a date with just

Re: [R] Plotting in R

2019-07-12 Thread Jim Lemon
t;array", > > tickangle = 270 > > )) > > > > But the chart didn't show any tick labels. > > I guess I need to sample sydf$monthday, right? Because that's what I want > > to show as tick labels. But the problem is that monthday is string, and

Re: [R] Plotting in R

2019-07-12 Thread Jim Lemon
t to > show as tick labels. But the problem is that monthday is string, and can't > use a value for "by=", maybe I need to sample somehow by the index position. > > Thanks, > Steven > > -Original Message- > From: Jim Lemon > Sent: Thursday, Jul

Re: [R] Plotting in R

2019-07-12 Thread nstefi
value for "by=", maybe I need to sample somehow by the index position. Thanks, Steven -Original Message- From: Jim Lemon Sent: Thursday, July 11, 2019 10:41 PM To: nst...@gmail.com Cc: r-help mailing list Subject: Re: [R] Plotting in R Hi Steven, Neat solution. With a lot m

Re: [R] Plotting in R

2019-07-11 Thread Jim Lemon
ues evenly from the list of x axis lables, and > use that for the "ticktext" parameter. > I thought it must be some variation of the seq(from, to, by= ). Can I use > that with a list of strings? > > Thanks, > Steven > > -Original Message- > From: Jim Lem

Re: [R] Plotting in R

2019-07-11 Thread nstefi
evenly from the list of x axis lables, and use that for the "ticktext" parameter. I thought it must be some variation of the seq(from, to, by= ). Can I use that with a list of strings? Thanks, Steven -Original Message- From: Jim Lemon Sent: Thursday, July 11, 2019 7:46 PM T

Re: [R] Plotting in R

2019-07-11 Thread Jim Lemon
want the > values on the x axis to show 05-01 06-01, etc. > Is that possible? > > Thanks, > Steven > > -Original Message- > From: R-help On Behalf Of Jim Lemon > Sent: Sunday, July 7, 2019 2:59 AM > To: Steven Yen ; r-help mailing list > > Subject: Re: [R]

Re: [R] Plotting in R

2019-07-11 Thread Bert Gunter
t; but this only changes the title of the x axis to "month-day". I want the > values on the x axis to show 05-01 06-01, etc. > Is that possible? > > Thanks, > Steven > > -Original Message- > From: R-help On Behalf Of Jim Lemon > Sent: Sunday, July 7, 2019 2:59 AM &g

Re: [R] Plotting in R

2019-07-11 Thread David Carlson
his: > plot(sydf$year,sydf$rate,type="b", > xlab="month-day",ylab="Rate") > > but this only changes the title of the x axis to "month-day". I want the > values on the x axis to show 05-01 06-01, etc. > Is that possible? > > Thanks,

Re: [R] Plotting in R

2019-07-11 Thread nstefi
ot_ly?" -Original Message- From: nst...@gmail.com Sent: Thursday, July 11, 2019 11:59 AM To: 'Jim Lemon' ; 'Steven Yen' ; 'r-help mailing list' Subject: RE: [R] Plotting in R Hi Jim, Thanks for your email. My question was: how to change the x axis labels without cha

Re: [R] Plotting in R

2019-07-11 Thread nstefi
, etc. Is that possible? Thanks, Steven -Original Message- From: R-help On Behalf Of Jim Lemon Sent: Sunday, July 7, 2019 2:59 AM To: Steven Yen ; r-help mailing list Subject: Re: [R] Plotting in R Hi Steven, A basic plot can be displayed like this: sydf<-read.table(text="year

Re: [R] Plotting in R

2019-07-07 Thread Jim Lemon
Hi Steven, A basic plot can be displayed like this: sydf<-read.table(text="year rate 1993 0.608 1994 0.622 1996 0.623 1998 0.647 2000 0.646 2002 0.625 2004 0.628 2006 0.685 2008 0.679 2010 0.595 2012 0.567 2014 0.599 2016 0.642 2018 0.685", header=TRUE) plot(sydf$year,sydf$rate,type=

Re: [R] Plotting in R

2019-07-06 Thread John Kane
Please do not post in html. You could use ggplot to do this. But you need to do a bit of work yourself. On Sat, 6 Jul 2019 at 10:51, wrote: > > Hello, > > Please don't post inHTML, the data is unreadable. > > As for the question, it is very basic. try any of > > > plot(rate ~ year, data = df)

Re: [R] Plotting in R

2019-07-06 Thread ruipbarradas
Hello, Please don't post inHTML, the data is unreadable. As for the question, it is very basic. try any of plot(rate ~ year, data = df)# df is your dataframe plot(df$year, df$rate) Then read ?plot and ?par to see how to customize the graph, by changing the plot type, how to add colors,

Re: [R] Plotting in R

2019-07-06 Thread Bert Gunter
Oh come on! Please do your homework and spend time with some basic R tutorials, one of which ships with R, although there are tons more good ones on the web. And FYI, there are *several* different plotting systems that one can access using various R packages. Probably the most basic -- but still

Re: [R] plotting an isosurface on a 3d plot

2019-06-17 Thread Duncan Murdoch
See responses inline. On 17/06/2019 1:18 p.m., ravi wrote: Hi Duncan, Once again, I must thank you for your excellent support. I am getting to know things which I would have been very difficult by just reading the manual. I have followed your suggestion to use the qmesh3d command. I have un

Re: [R] plotting an isosurface on a 3d plot

2019-06-17 Thread ravi via R-help
Hi Duncan,Once again, I must thank you for your excellent support. I am getting to know things which I would have been very difficult by just reading the manual. I have followed your suggestion to use the qmesh3d command. I have uniquely defined the vertices. I am still stuck. I show below my c

Re: [R] plotting an isosurface on a 3d plot

2019-06-14 Thread Duncan Murdoch
On 14/06/2019 9:14 a.m., ravi wrote: Hi Duncan, Thanks a lot for your help. You have really opened up a road for me to to pursue further. Your later solution with cylinder3d is interesting. However, in my real application, I have several parallel planes and very irregular contours in each of

Re: [R] plotting an isosurface on a 3d plot

2019-06-14 Thread ravi via R-help
Hi Duncan,Thanks a lot for your help. You have really opened up a road for me to to pursue further. Your later solution with cylinder3d is interesting. However, in my real application, I have several parallel planes and very irregular contours in each of them. So the quad3d command is more usef

Re: [R] plotting an isosurface on a 3d plot

2019-06-13 Thread Duncan Murdoch
On 13/06/2019 4:32 p.m., Duncan Murdoch wrote: On 13/06/2019 12:47 p.m., ravi via R-help wrote: Hi,I want to plot a surface joining a circle on a plane with another circle (a little offset w.r.t. the first one) on a parallel plane. This is a very simplified version of my problem. I will explai

Re: [R] plotting an isosurface on a 3d plot

2019-06-13 Thread Duncan Murdoch
On 13/06/2019 12:47 p.m., ravi via R-help wrote: Hi,I want to plot a surface joining a circle on a plane with another circle (a little offset w.r.t. the first one) on a parallel plane. This is a very simplified version of my problem. I will explain with the following code : # First, I plot the

Re: [R] Plotting more than one regression line in ggplot

2019-06-06 Thread rain1290--- via R-help
Hi Rui, Yes! This worked just fine! Thank you so, so much for your time and patience!  -Original Message- From: Rui Barradas To: rain1290 ; r-help Sent: Thu, Jun 6, 2019 3:25 pm Subject: Re: [R] Plotting more than one regression line in ggplot Hello, Try this. values_to_plot <

Re: [R] Plotting more than one regression line in ggplot

2019-06-06 Thread Rui Barradas
N, would I do something like this? : ggplot(subset(NewestdataUltra, L1 != 'onepctCO2MEDIAN'), aes(x, value, colour = L1)) + geom_point() + scale_color_manual(values =c("green", "blue" "red", "black")) + geom_smooth(method = lm, se=FALSE) **/

Re: [R] Plotting more than one regression line in ggplot

2019-06-06 Thread rain1290--- via R-help
scale_color_manual(values =c("green", "blue" "red", "black")) + geom_smooth(method = lm, se=FALSE) Thanks, -Original Message----- From: Rui Barradas To: rain1290 ; r-help Sent: Thu, Jun 6, 2019 11:53 am Subject: Re: [R] Plotting more than one regression l

Re: [R] Plotting more than one regression line in ggplot

2019-06-06 Thread Rui Barradas
, "blue" "red")) + geom_smooth(method = lm, se=FALSE) **//___^ **//___^I still end up with the same error, however, when I specify only 3 colors. Why could this be? -Original Message- From: Rui Barradas To: rain1290 ; r-help Sent: Thu, Jun 6, 2019 11:18 am Subject

Re: [R] Plotting more than one regression line in ggplot

2019-06-06 Thread rain1290--- via R-help
+ geom_smooth(method = lm, se=FALSE) I still end up with the same error, however, when I specify only 3 colors. Why could this be? -Original Message- From: Rui Barradas To: rain1290 ; r-help Sent: Thu, Jun 6, 2019 11:18 am Subject: Re: [R] Plotting more than one regression line in ggp

Re: [R] Plotting more than one regression line in ggplot

2019-06-06 Thread Rui Barradas
quot; "red"" **//___^ Why would this error appear?  I think that I assigned the colors correctly to each of the four objects in question, so why would this occur? Thank you, once again! -Original Message- From: Rui Barradas To: rain1290 ; r-help Sent: Thu, Jun 6, 201

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