R lattice stripplot add median line to data

Hi

This essentially has transformed the stripplot into a boxplot...

NO

I wrote:

***after*** your lattice plot just do...

and I ment issue addLine after the stripplot is plotted.

So first

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
)

than

addLine(h=aggregate(df$Aboundance, list(df$Group), median)$x, once=T)

Cheers
Petr

-----Original Message-----
From: Luigi Marongiu <marongiu.luigi at gmail.com>
Sent: Friday, October 25, 2019 11:24 AM
To: PIKAL Petr <petr.pikal at precheza.cz>
Cc: Bert Gunter <bgunter.4567 at gmail.com>; r-help <r-help at r-project.org>
Subject: Re: [R] R lattice stripplot add median line to data

This essentially has transformed the stripplot into a boxplot...

On Fri, Oct 25, 2019 at 11:19 AM PIKAL Petr <petr.pikal at precheza.cz> wrote:

Hi

I asked similar question few yeas ago (in different context) and besed
on answers I made custom function which adds line after the lattice
graph is plotted.

after your lattice plot just do

addLine(h=aggregate(df$Aboundance, list(df$Group), median)$x, once=T)

the function is defined as follows

addLine <- function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once
= F) {
    tcL <- trellis.currentLayout()
    k <- 0
    for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
        j] > 0) {
        k <- k + 1
        trellis.focus("panel", j, i, highlight = FALSE)
        if (once)
            panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
                ...)
        else panel.abline(a = a, b = b, v = v, h = h, ...)
        trellis.unfocus()
    }
  }

Cheers
Petr

-----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

how

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

use

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

variables are

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

horizontal

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",

"brown3"))),

   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

= meds[i],

                  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,

4,

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

1,

               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

      [[alternative HTML version deleted]]

--
Best regards,
Luigi