Ops, yes now it works. But again it gives a single value for each
class (normal, tumour, metastasis).
On Fri, Oct 25, 2019 at 1:27 PM PIKAL Petr <petr.pi...@precheza.cz> wrote:
>
> 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.lu...@gmail.com>
> > Sent: Friday, October 25, 2019 11:24 AM
> > To: PIKAL Petr <petr.pi...@precheza.cz>
> > Cc: Bert Gunter <bgunter.4...@gmail.com>; r-help <r-help@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.pi...@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-boun...@r-project.org> On Behalf Of Bert Gunter
> > > > Sent: Thursday, October 24, 2019 6:23 PM
> > > > To: Luigi Marongiu <marongiu.lu...@gmail.com>
> > > > Cc: r-help <r-help@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.lu...@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@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@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
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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