R lattice stripplot add median line to data

-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Bert Gunter
Sent: Thursday, October 24, 2019 6:23 PM
To: Luigi Marongiu <marongiu.luigi at gmail.com>
Cc: r-help <r-help at r-project.org>
Subject: Re: [R] R lattice stripplot add median line to data

Yes, it's possible to do about anything in lattice, but you have to learn

to write custom panel functions, which takes some effort. If you want to

lattice in this way, you should probably go through Deepayan's book.

Here is one way to do what I think you want. Note that it depends on
knowing that when the x axis is a factor, the x positions of the y

at 1, 2, 3, .. etc (to the number of levels of the factor) to draw the

line segments. This is documented somewhere, but I don't remember where.

stripplot(
   Aboundance ~ Taxon|Group,
   df,
   groups = Taxon,
   scales=list(y=list(log=T)),
   pch=16,  cex = 1.5,
   ylab = expression(bold("Number of taxons")),
   jitter.data = TRUE,
   layout=c(3,1),
   col = "black",
   # colour panels differently
   par.settings=list(strip.background=list(col=c("darkorchid3",
                                                 "darkolivegreen3",

   strip = function(...,bg) {
      strip.default(...,
                    bg =
trellis.par.get("strip.background")$col[which.packet()])
      },
   panel = function(x,y,...){
      panel.stripplot(x,y,...)
      lev <- seq_along(levels(x))
      meds <- tapply(y,x,median,na.rm = TRUE)
      for(i in lev)panel.segments(x0 = i-.25, y0 = meds[i], x1 = i+.25, y1

                  lwd=2,col = "red")
   }
)

Cheers,
Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Oct 24, 2019 at 2:22 AM Luigi Marongiu
<marongiu.luigi at gmail.com>
wrote:

Dear all,
I am plotting data with lattice's stripplot. Is it possible to add a
median line to each cluster?
This is the working example:

```
Sample =  c("A0", "A0", "A0", "A3", "A3", "A3", "A7", "A7", "A7",
            "A9", "A9", "A9", "H1", "H1",
            "H1", "H2", "H2", "H2", "H3", "H3", "H3", "P1", "P1", "P1",
            "P2", "P2", "P2", "P3",
            "P3", "P3", "P4", "P4", "P4", "P5", "P5", "P5", "P7", "P7",
            "P7", "A0", "A0", "A0",
            "A3", "A3", "A3", "A7", "A7", "A7", "A9", "A9", "A9", "H1",
            "H1", "H1", "H2", "H2",
            "H2", "H3", "H3", "H3", "P1", "P1", "P1", "P2", "P2", "P2",
            "P3", "P3", "P3", "P4",
            "P4", "P4", "P5", "P5", "P5", "P7", "P7", "P7") Group =
rep(c("Normal", "Tumour",  "Metastasis" ), 26) Taxon =
c(rep("Microviridae", 39), rep("Caudovirales", 39))
Aboundance = c(0, 151,   3,   0, 102, 509,   4,   1, 277,   4,  87,   7,
               16,  13,  22,  47,  12,   1,
                5, 251,   4,   8,   4,   2,  14,   4,   2,  10,   4,

               13,   1,   1,   5,   7,   2,   6,   6,   4,   1,   2,

               2,   1,   2,   0,   0,   2,   0,   0,   1,   0,   0,   0,
               0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,
               0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0)
df = data.frame(Sample, Group, Taxon, Aboundance,
                stringsAsFactors = FALSE)
library(lattice)
stripplot(
  Aboundance ~ Taxon|Group,
  df,
  groups = Taxon,
  scales=list(y=list(log=T)),
  pch=16,  cex = 1.5,
  ylab = expression(bold("Number of taxons")),
  jitter.data = TRUE,
  layout=c(3,1),
  col = "black",
  # colour panels differently
  par.settings=list(strip.background=list(col=c("darkorchid3",
                                                "darkolivegreen3",
"brown3"))),
  strip = function(..., bg) {
    strip.default(...,
                  bg =
trellis.par.get("strip.background")$col[which.packet()])
  },
  # add median bar
)
```

Thank you
--
Best regards,
Luigi

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