Hi Richard Yes you are right, I did not check my answer enough.
Cheers Petr > -----Original Message----- > From: Richard M. Heiberger [mailto:r...@temple.edu] > Sent: Monday, February 12, 2018 6:10 PM > To: PIKAL Petr <petr.pi...@precheza.cz> > Cc: greg holly <mak.hho...@gmail.com>; r-help mailing list <r-help@r- > project.org> > Subject: Re: [R] plotting the regression coefficients > > Petr, there was a thinko in your response. > > > tmp <- data.frame(m=factor(letters[1:4]), n=1:4) tmp tmp$m <- factor(tmp$m, > levels=c("c","b","a","d")) ## right tmp[order(tmp$m),] > > tmp <- data.frame(m=factor(letters[1:4]), n=1:4) > levels(tmp$m) <- c("c","b","a","d") ## wrong tmp[order(tmp$m),] > > changing levels directly changes the names only, not the ordering. > You must redefine the factor to retain the relationship of factor names with > the > numerical values. > > Rich > > > On Mon, Feb 12, 2018 at 3:49 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote: > > Hi > > > > After melt you can change levels of your factor variable. Again with the toy > example. > > > >> levels(temp$variable) > > [1] "y1" "y2" "y3" "y4" > >> levels(temp$variable) <- levels(temp$variable)[c(2,4,1,3)] > >> levels(temp$variable) > > [1] "y2" "y4" "y1" "y3" > >> > > > > And you will get graphs with this new levels ordering. > > > > Cheers > > Petr > > > > From: greg holly [mailto:mak.hho...@gmail.com] > > Sent: Monday, February 12, 2018 8:52 AM > > To: PIKAL Petr <petr.pi...@precheza.cz> > > Cc: r-help mailing list <r-help@r-project.org> > > Subject: Re: [R] plotting the regression coefficients > > > > Hi Petr; > > > > Thanks so much. This is great! Although last Sunday, alternatively, I have > solved the problem using the following statement at the very end of the > program. > > > > ggsave('circle.pdf', p4, height = 70, width = 8, device=pdf, limitsize = F, > dpi=300). > > > > This works very well too. > > > > Asa my categorical variables are in my Y axis, my R program reorders the > names on Y-axis. However, I would like have and plot output with the names as > they are. Is there any way to have plot without ordering the names of > variables > on Y-axis? > > > > Regards, > > Greg. > > > > On Mon, Feb 12, 2018 at 10:12 AM, PIKAL Petr > <petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote: > > Hi > > > > Maybe there are other ways but I would split data to several chunks e.g. in > list and use for cycle to fill multipage pdf. > > > > With the toy data something like > > > > library(reshape2) > > library(ggplot2) > > temp <- melt(temp) > > temp.s<-split(temp, cut(1:nrow(temp), 2)) > > > > pdf("temp.pdf") > > for (i in 1: length(temp.s)) { > > p <- ggplot(temp.s[[i]], aes(x=par1, y=variable, size=abs(value), > > colour=factor(sign(value)))) > > print(p+geom_point()) > > } > > dev.off() > > > > But the real code partly depends on your real data. > > > > Cheers > > Petr > > > > From: greg holly > > [mailto:mak.hho...@gmail.com<mailto:mak.hho...@gmail.com>] > > Sent: Saturday, February 10, 2018 9:05 PM > > > > To: PIKAL Petr <petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> > > Cc: r-help mailing list > > <r-help@r-project.org<mailto:r-help@r-project.org>> > > Subject: Re: [R] plotting the regression coefficients > > > > Hi Peter; > > > > The R code you provided works very well. Once again thanks so much for this. > The number of variables in my data set that should appear on the y-axis is 733 > and they are not numerical (for example the name of one variable is palmitoyl- > arachidonoyl-glycerol (16:0/20:4) [1]*. So, the plot looks very messy in one > page. How can I make the plot to print out on multiple pages? > > > > Regards, > > > > Greg > > > > On Thu, Feb 8, 2018 at 4:33 PM, greg holly > <mak.hho...@gmail.com<mailto:mak.hho...@gmail.com>> wrote: > > Hi Petr; > > > > Thanks so much. Exactly this is what I need. I will play to change color > > and so > on but this backbound is perfect to me. I do appreciate your help and support. > > > > Regards, > > Greg > > > > On Thu, Feb 8, 2018 at 1:29 PM, PIKAL Petr > <petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote: > > Hi > > I copied your values to R, here it is > > > >> dput(temp) > > > > temp <- structure(list(par1 = structure(1:4, .Label = c("x1", "x2", > > "x3", "x4"), class = "factor"), y1 = c(-0.19, 0.45, -0.09, -0.16), > > y2 = c(0.4, -0.75, 0.14, -0.01), y3 = c(-0.06, -8.67, 1.42, > > 2.21), y4 = c(0.13, -0.46, 0.06, 0.06)), .Names = c("par1", "y1", > > "y2", "y3", "y4"), class = "data.frame", row.names = c(NA, > > -4L)) > > > > For plotting it need to be reshaped > > > > library(reshape2) > > library(ggplot2) > > > > temp <- melt(temp) > > p <- ggplot(temp, aes(x=par1, y=variable, size=abs(value), > > colour=factor(sign(value)))) > > p+geom_point() > > > > Is this what you wanted? > > > > Cheers > > Petr > > And preferably do not post in HTML, the email content could be scrambled. > > > > From: greg holly > > [mailto:mak.hho...@gmail.com<mailto:mak.hho...@gmail.com>] > > Sent: Thursday, February 8, 2018 9:23 AM > > To: PIKAL Petr <petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> > > Cc: r-help mailing list > > <r-help@r-project.org<mailto:r-help@r-project.org>> > > Subject: Re: [R] plotting the regression coefficients > > > > Hi Petr; > > > > Thanks for your reply. It is much appreciated. A small example is > > given below for 4 independent and 4 dependent variables only. The > > values given are regression coefficients.I have looked ggplot > > documents before writing to you. Unfortunately, I could not figure out > > as my experience in ggplot is ignorable > > > > Regards. > > Greg > > > > y1 y2 y3 y4 > > x1 -0.19 0.40 -0.06 0.13 > > x2 0.45 -0.75 -8.67 -0.46 > > x3 -0.09 0.14 1.42 0.06 > > x4 -0.16 -0.01 2.21 0.06 > > > > > > On Thu, Feb 8, 2018 at 10:19 AM, PIKAL Petr > <petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote: > > Hi > > > > Example, example, example - preferably working. > > > > Wild guess - did you try ggplot? > > > > Cheers > > Petr > > > > > >> -----Original Message----- > >> From: R-help > >> [mailto:r-help-boun...@r-project.org<mailto:r-help-bounces@r-project. > >> org>] On Behalf Of greg holly > >> Sent: Thursday, February 8, 2018 8:14 AM > >> To: r-help mailing list > >> <r-help@r-project.org<mailto:r-help@r-project.org>> > >> Subject: [R] plotting the regression coefficients > >> > >> Hi Dear all; > >> > >> I would like to create a plot for regression coefficients with each > >> independent variable (x) along the side and the phenotypes (y) across > >> the top (as given below). For each data point, direction and > >> magnitude of effect could be color and significance could be the size of > >> the > circle? Is this possible? > >> > >> > >> I would greatly be appreciated your help. > >> > >> Thanks, > >> > >> Greg > >> > >> > >> > >> y1 y2 y3 y4 y5 y6 > >> x1 > >> x2 > >> x3 > >> x4 > >> x5 > >> x6 > >> x7 > >> x8 > >> x9 > >> x10 > >> x11 > >> x12 > >> x13 > >> x14 > >> x15 > >> x16 > >> x17 > >> . > >> . > >> > > > > ________________________________ Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. 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