[R] R lattice stripplot add median line to data

[PIKAL Petr]

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 using r-project.org> On Behalf Of Bert Gunter
> Sent: Thursday, October 24, 2019 6:23 PM
> To: Luigi Marongiu <marongiu.luigi using gmail.com>
> Cc: r-help <r-help using 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 using 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
> >
> > ______________________________________________
> > 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.
> >
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> 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.