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Luigi Marongiu

2020-Sep-23 12:47 UTC

[R] package plotrix: how to account for two two z categories

Hello,
I have an experiment measuring optical density (OD) when comparing
three parameters:
a) concentration of the target
b) concentration of the probe
c) concentration of the reporter antibody.
Using plotrix I can nicely draw the first two into clusters, but I
can't get separation for the third parameter. is there a way in
plotrix to custer data according to two, let's say, z parameters (I
call the second high-level parameter as w)? For instance, two
clusters, each separated into two subclusters. Or is this more a job
for lattice?
Thank you.

```
x = rep(c(rep("1000 pmol", 4), rep("0 pmol", 4)),2)
z =  rep(c(rep("Treated", 2), rep("Untreated", 2),
rep("Treated", 2),
rep("Untreated", 2)))
w = c(rep("1:1000", 8), rep("1:2000", 8))
y = c(1.18, 1.22, 1.52, 2.37, 0.97, 1.08, 1.17, 1.58, 1.16, 1.16, 2.27, 2.24,
      1.26, 1.28, 1.39, 1.77)
Q = data.frame(x, z, w, y, stringsAsFactors = FALSE)
names(Q) = c("[Target]", "Enzyme", "[Antibody]",
"OD")
names(Q) = c("x", "z", "w", "y") # for
ease, I'll use single letters
library(plotrix)
brkdn.plot(y~x+z, data=Q,
           pch = c(1, 16), cex = 1.5, type="p",
           main="Single Measurement",
           xlab=expression(bold("S1 nuclease")),
           ylab=expression(bold("Optical density")))
brkdn.plot(y~x+z+w, data=Q,
           pch = c(1, 16), cex = 1.5, type="p",
           main="Double Measurement",
           xlab=expression(bold("S1 nuclease")),
           ylab=expression(bold("Optical density")))
```

Jim Lemon

2020-Sep-24 07:29 UTC

head link

[R] package plotrix: how to account for two two z categories

Hi Luigi,
To display a nested breakdown like this I would suggest barNest. This
is one way to display the nesting. Note that if you change the order
of the factors in the formula you will get a different plot, so think
about how you want the summaries nested. Error bars can only be
displayed on the final breakdown.

# because you have fairly long labels, use a wide plot
x11(width=10)
barcol<-list("lightgray",c("#ff00ff","#ff99ff"),
 c("#00ff00","#66ff66"),c("#aaaa00","#888800"))
barNest(y~x+z+w,Q,main="Double Measurement",
 ylab="Response",col=barcol,errbars=TRUE)

Jim

On Wed, Sep 23, 2020 at 10:48 PM Luigi Marongiu
<marongiu.luigi at gmail.com> wrote:>
> Hello,
> I have an experiment measuring optical density (OD) when comparing
> three parameters:
> a) concentration of the target
> b) concentration of the probe
> c) concentration of the reporter antibody.
> Using plotrix I can nicely draw the first two into clusters, but I
> can't get separation for the third parameter. is there a way in
> plotrix to custer data according to two, let's say, z parameters (I
> call the second high-level parameter as w)? For instance, two
> clusters, each separated into two subclusters. Or is this more a job
> for lattice?
> Thank you.
>
> ```
> x = rep(c(rep("1000 pmol", 4), rep("0 pmol", 4)),2)
> z =  rep(c(rep("Treated", 2), rep("Untreated", 2),
rep("Treated", 2),
> rep("Untreated", 2)))
> w = c(rep("1:1000", 8), rep("1:2000", 8))
> y = c(1.18, 1.22, 1.52, 2.37, 0.97, 1.08, 1.17, 1.58, 1.16, 1.16, 2.27,
2.24,
>       1.26, 1.28, 1.39, 1.77)
> Q = data.frame(x, z, w, y, stringsAsFactors = FALSE)
> names(Q) = c("[Target]", "Enzyme",
"[Antibody]", "OD")
> names(Q) = c("x", "z", "w", "y") #
for ease, I'll use single letters
> library(plotrix)
> brkdn.plot(y~x+z, data=Q,
>            pch = c(1, 16), cex = 1.5, type="p",
>            main="Single Measurement",
>            xlab=expression(bold("S1 nuclease")),
>            ylab=expression(bold("Optical density")))
> brkdn.plot(y~x+z+w, data=Q,
>            pch = c(1, 16), cex = 1.5, type="p",
>            main="Double Measurement",
>            xlab=expression(bold("S1 nuclease")),
>            ylab=expression(bold("Optical density")))
> ```
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Jim Lemon

2020-Sep-24 08:32 UTC

head link

[R] package plotrix: how to account for two two z categories

Hi Luigi,
I thought a lot about that when I was writing the function. The only
way I could think of to show the nesting was dots with horizontal
lines and it looked messy and was quite hard to visualize the nesting.
If you do have any great ideas I always welcome contributions to
plotrix.

Jim

On Thu, Sep 24, 2020 at 6:25 PM Luigi Marongiu <marongiu.luigi at
gmail.com> wrote:>
> Thank you Jim, that is really nice!
> But is there a way to use dots instead of boxes? and how do I control
> the colours?
> Best regards
> Luigi
>
> On Thu, Sep 24, 2020 at 9:29 AM Jim Lemon <drjimlemon at gmail.com>
wrote:
> >
> > Hi Luigi,
> > To display a nested breakdown like this I would suggest barNest. This
> > is one way to display the nesting. Note that if you change the order
> > of the factors in the formula you will get a different plot, so think
> > about how you want the summaries nested. Error bars can only be
> > displayed on the final breakdown.
> >
> > # because you have fairly long labels, use a wide plot
> > x11(width=10)
> >
barcol<-list("lightgray",c("#ff00ff","#ff99ff"),
> > 
c("#00ff00","#66ff66"),c("#aaaa00","#888800"))
> > barNest(y~x+z+w,Q,main="Double Measurement",
> >  ylab="Response",col=barcol,errbars=TRUE)
> >
> > Jim
> >
> > On Wed, Sep 23, 2020 at 10:48 PM Luigi Marongiu
> > <marongiu.luigi at gmail.com> wrote:
> > >
> > > Hello,
> > > I have an experiment measuring optical density (OD) when
comparing
> > > three parameters:
> > > a) concentration of the target
> > > b) concentration of the probe
> > > c) concentration of the reporter antibody.
> > > Using plotrix I can nicely draw the first two into clusters, but
I
> > > can't get separation for the third parameter. is there a way
in
> > > plotrix to custer data according to two, let's say, z
parameters (I
> > > call the second high-level parameter as w)? For instance, two
> > > clusters, each separated into two subclusters. Or is this more a
job
> > > for lattice?
> > > Thank you.
> > >
> > > ```
> > > x = rep(c(rep("1000 pmol", 4), rep("0 pmol",
4)),2)
> > > z =  rep(c(rep("Treated", 2),
rep("Untreated", 2), rep("Treated", 2),
> > > rep("Untreated", 2)))
> > > w = c(rep("1:1000", 8), rep("1:2000", 8))
> > > y = c(1.18, 1.22, 1.52, 2.37, 0.97, 1.08, 1.17, 1.58, 1.16, 1.16,
2.27, 2.24,
> > >       1.26, 1.28, 1.39, 1.77)
> > > Q = data.frame(x, z, w, y, stringsAsFactors = FALSE)
> > > names(Q) = c("[Target]", "Enzyme",
"[Antibody]", "OD")
> > > names(Q) = c("x", "z", "w",
"y") # for ease, I'll use single letters
> > > library(plotrix)
> > > brkdn.plot(y~x+z, data=Q,
> > >            pch = c(1, 16), cex = 1.5, type="p",
> > >            main="Single Measurement",
> > >            xlab=expression(bold("S1 nuclease")),
> > >            ylab=expression(bold("Optical density")))
> > > brkdn.plot(y~x+z+w, data=Q,
> > >            pch = c(1, 16), cex = 1.5, type="p",
> > >            main="Double Measurement",
> > >            xlab=expression(bold("S1 nuclease")),
> > >            ylab=expression(bold("Optical density")))
> > > ```
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible
code.
>
>
>
> --
> Best regards,
> Luigi

Jim Lemon

2020-Sep-24 08:34 UTC

head link

[R] package plotrix: how to account for two two z categories

Oh, sorry, forgot about the colors. A list beginning with the color
for the overall summary, then colors for the first factor and so on.
See the help page for examples.

Jim

On Thu, Sep 24, 2020 at 6:32 PM Jim Lemon <drjimlemon at gmail.com>
wrote:>
> Hi Luigi,
> I thought a lot about that when I was writing the function. The only
> way I could think of to show the nesting was dots with horizontal
> lines and it looked messy and was quite hard to visualize the nesting.
> If you do have any great ideas I always welcome contributions to
> plotrix.
>
> Jim
>
> On Thu, Sep 24, 2020 at 6:25 PM Luigi Marongiu <marongiu.luigi at
gmail.com> wrote:
> >
> > Thank you Jim, that is really nice!
> > But is there a way to use dots instead of boxes? and how do I control
> > the colours?
> > Best regards
> > Luigi
> >
> > On Thu, Sep 24, 2020 at 9:29 AM Jim Lemon <drjimlemon at
gmail.com> wrote:
> > >
> > > Hi Luigi,
> > > To display a nested breakdown like this I would suggest barNest.
This
> > > is one way to display the nesting. Note that if you change the
order
> > > of the factors in the formula you will get a different plot, so
think
> > > about how you want the summaries nested. Error bars can only be
> > > displayed on the final breakdown.
> > >
> > > # because you have fairly long labels, use a wide plot
> > > x11(width=10)
> > >
barcol<-list("lightgray",c("#ff00ff","#ff99ff"),
> > > 
c("#00ff00","#66ff66"),c("#aaaa00","#888800"))
> > > barNest(y~x+z+w,Q,main="Double Measurement",
> > >  ylab="Response",col=barcol,errbars=TRUE)
> > >
> > > Jim
> > >
> > > On Wed, Sep 23, 2020 at 10:48 PM Luigi Marongiu
> > > <marongiu.luigi at gmail.com> wrote:
> > > >
> > > > Hello,
> > > > I have an experiment measuring optical density (OD) when
comparing
> > > > three parameters:
> > > > a) concentration of the target
> > > > b) concentration of the probe
> > > > c) concentration of the reporter antibody.
> > > > Using plotrix I can nicely draw the first two into clusters,
but I
> > > > can't get separation for the third parameter. is there a
way in
> > > > plotrix to custer data according to two, let's say, z
parameters (I
> > > > call the second high-level parameter as w)? For instance,
two
> > > > clusters, each separated into two subclusters. Or is this
more a job
> > > > for lattice?
> > > > Thank you.
> > > >
> > > > ```
> > > > x = rep(c(rep("1000 pmol", 4), rep("0
pmol", 4)),2)
> > > > z =  rep(c(rep("Treated", 2),
rep("Untreated", 2), rep("Treated", 2),
> > > > rep("Untreated", 2)))
> > > > w = c(rep("1:1000", 8), rep("1:2000",
8))
> > > > y = c(1.18, 1.22, 1.52, 2.37, 0.97, 1.08, 1.17, 1.58, 1.16,
1.16, 2.27, 2.24,
> > > >       1.26, 1.28, 1.39, 1.77)
> > > > Q = data.frame(x, z, w, y, stringsAsFactors = FALSE)
> > > > names(Q) = c("[Target]", "Enzyme",
"[Antibody]", "OD")
> > > > names(Q) = c("x", "z", "w",
"y") # for ease, I'll use single letters
> > > > library(plotrix)
> > > > brkdn.plot(y~x+z, data=Q,
> > > >            pch = c(1, 16), cex = 1.5, type="p",
> > > >            main="Single Measurement",
> > > >            xlab=expression(bold("S1 nuclease")),
> > > >            ylab=expression(bold("Optical
density")))
> > > > brkdn.plot(y~x+z+w, data=Q,
> > > >            pch = c(1, 16), cex = 1.5, type="p",
> > > >            main="Double Measurement",
> > > >            xlab=expression(bold("S1 nuclease")),
> > > >            ylab=expression(bold("Optical
density")))
> > > > ```
> > > >
> > > > ______________________________________________
> > > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > > > and provide commented, minimal, self-contained, reproducible
code.
> >
> >
> >
> > --
> > Best regards,
> > Luigi

R help - Sep 2020 - package plotrix: how to account for two two z categories

[R] package plotrix: how to account for two two z categories

[R] package plotrix: how to account for two two z categories

[R] package plotrix: how to account for two two z categories

[R] package plotrix: how to account for two two z categories