# Re: [R] plotting the regression coefficients

```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-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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