[R] plotting the regression coefficients

PIKAL Petr petr.pikal at precheza.cz
Tue Feb 13 15:34:21 CET 2018

```Hi
should do the trick.
Actually I found it by Google
ggplot colour
http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/
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.hholly at gmail.com]
Sent: Monday, February 12, 2018 7:07 PM
To: Richard M. Heiberger <rmh at temple.edu>
Cc: PIKAL Petr <petr.pikal at precheza.cz>; r-help mailing list <r-help at 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 <rmh at temple.edu<mailto:rmh at 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.pikal at precheza.cz<mailto:petr.pikal at 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.hholly at gmail.com<mailto:mak.hholly at gmail.com>]
> Sent: Monday, February 12, 2018 8:52 AM
> To: PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>>
> Cc: r-help mailing list <r-help at r-project.org<mailto:r-help at 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.pikal at precheza.cz<mailto:petr.pikal at precheza.cz><mailto:petr.pikal at precheza.cz<mailto:petr.pikal at 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.hholly at gmail.com<mailto:mak.hholly at gmail.com><mailto:mak.hholly at gmail.com<mailto:mak.hholly at gmail.com>>]
> Sent: Saturday, February 10, 2018 9:05 PM
>
> To: PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz><mailto:petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>>>
> Cc: r-help mailing list <r-help at r-project.org<mailto:r-help at r-project.org><mailto:r-help at r-project.org<mailto:r-help at 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.hholly at gmail.com<mailto:mak.hholly at gmail.com><mailto:mak.hholly at gmail.com<mailto:mak.hholly at 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.pikal at precheza.cz<mailto:petr.pikal at precheza.cz><mailto:petr.pikal at precheza.cz<mailto:petr.pikal at 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.hholly at gmail.com<mailto:mak.hholly at gmail.com><mailto:mak.hholly at gmail.com<mailto:mak.hholly at gmail.com>>]
> Sent: Thursday, February 8, 2018 9:23 AM
> To: PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz><mailto:petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>>>
> Cc: r-help mailing list <r-help at r-project.org<mailto:r-help at r-project.org><mailto:r-help at r-project.org<mailto:r-help at 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.pikal at precheza.cz<mailto:petr.pikal at precheza.cz><mailto:petr.pikal at precheza.cz<mailto:petr.pikal at 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-bounces at r-project.org<mailto:r-help-bounces at r-project.org><mailto:r-help-bounces at r-project.org<mailto:r-help-bounces at r-project.org>>] On Behalf Of greg holly
>> Sent: Thursday, February 8, 2018 8:14 AM
>> To: r-help mailing list <r-help at r-project.org<mailto:r-help at r-project.org><mailto:r-help at r-project.org<mailto:r-help at 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
>> .
>> .
>>

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