Hi Petr; Thanks for this. I have used scale_colour_gradient before but could not get what I am looking for. I will check the links you provide to get Idea. Once again thanks for your support and help.
Rgerads, Greg On Tue, Feb 13, 2018 at 5:34 PM, PIKAL Petr <petr.pi...@precheza.cz> wrote: > Hi > > scale_colour_gradient(“red”, “blue”) > > should do the trick. > > Actually I found it by Google > > ggplot colour > > http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/ > > http://www.sthda.com/english/wiki/ggplot2-colors-how-to- > change-colors-automatically-and-manually#gradient-colors-for-scatter-plots > > question. So you could find it too and probably far more quickly then > myself as I have also other duties. > > Cheers > > Petr > > BTW, you still post in HTML which could be sometimes problematic in this > text only list. > > > > *From:* greg holly [mailto:mak.hho...@gmail.com] > *Sent:* Monday, February 12, 2018 7:07 PM > *To:* Richard M. Heiberger <r...@temple.edu> > *Cc:* PIKAL Petr <petr.pi...@precheza.cz>; r-help mailing list < > r-help@r-project.org> > > *Subject:* Re: [R] plotting the regression coefficients > > > > Hi Petr and Richard; > > > > Thanks for your responses and supports. I just faced a different problem. > I have the following R codes and work well. > > > > p <- ggplot(a, aes(x=Phenotypes, y=Metabolites, size=abs(Beta), > colour=factor(sign(Beta)))) + > > theme(axis.text=element_text(size = 5)) > > p1<-p+geom_point() > > p2<-p1+theme(panel.grid.major = element_blank(), > > panel.grid.minor = element_blank(), > > panel.border = element_blank(), > > axis.ticks = element_blank()) > > > > p3<-p2+theme(panel.grid.major = element_blank(), panel.grid.minor = > element_blank(), > > panel.background = element_blank(), axis.line = element_line(colour = > "black")) > > > > p4<-p3+scale_color_manual(breaks = c("-1", "0", "1"), > > values=c("darkblue", "green", "red")) > > > > > > *My question is:* > > What if I was to repeat the analysis and standardize the beta (z-score) so > they are comparable across phenotypes (I have 8 phenotypes). We could then > “bin” the betas to represent shades of red and blue. > > > > Regards, > > > > Greg > > > > > > On Mon, Feb 12, 2018 at 8:10 PM, Richard M. Heiberger <r...@temple.edu> > wrote: > > 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 > -h...@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 > -h...@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- > boun...@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 > -h...@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. 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