After melt you can change levels of your factor variable. Again with the toy 

> 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.


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, 

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 


On Mon, Feb 12, 2018 at 10:12 AM, PIKAL Petr 
<petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote:

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

temp <- melt(temp)
temp.s<-split(temp, cut(1:nrow(temp), 2))

for (i in 1: length(temp.s)) {
p <- ggplot(temp.s[[i]], aes(x=par1, y=variable, size=abs(value), 

But the real code partly depends on your real data.


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?



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.


On Thu, Feb 8, 2018 at 1:29 PM, PIKAL Petr 
<petr.pi...@precheza.cz<mailto:petr.pi...@precheza.cz>> wrote:
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,

For plotting it need to be reshaped


temp <- melt(temp)
p <- ggplot(temp, aes(x=par1, y=variable, size=abs(value), 

Is this what you wanted?

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


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:

Example, example, example - preferably working.

Wild guess - did you try ggplot?


> -----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-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
> .
> .

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