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

[Luigi Marongiu]

Thanks! looks nicer already.
I am attaching the figure I temporarily made with normal brkdn.plot
but yours has more information.
Best regards
Luigi

On Fri, Sep 25, 2020 at 1:43 PM Jim Lemon <drjimlemon using gmail.com> wrote:
>
> Hi Luigi,
> Here is a quick example of how points would look in the same
> configuration. Perhaps with end caps to show the nesting it may be
> more like what you want.
>
> Jim
>
> On Thu, Sep 24, 2020 at 6:34 PM Jim Lemon <drjimlemon using gmail.com> wrote:
> >
> > 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 using 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 using 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 using 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 using 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 using 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



-- 
Best regards,
Luigi

-------------- next part --------------
A non-text attachment was scrubbed...
Name: Rplot.png
Type: image/png
Size: 10203 bytes
Desc: not available
URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20200925/63705b08/attachment.png>