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")))
```

--
Best regards,
Luigi