[R] R lattice stripplot add median line to data
PIKAL Petr
petr@p|k@| @end|ng |rom prechez@@cz
Fri Oct 25 13:27:34 CEST 2019
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 using gmail.com>
> Sent: Friday, October 25, 2019 11:24 AM
> To: PIKAL Petr <petr.pikal using precheza.cz>
> Cc: Bert Gunter <bgunter.4567 using gmail.com>; r-help <r-help using 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 using 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 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.
>
>
>
> --
> Best regards,
> Luigi
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