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")$col[which.packet()])
> > },
> > # add median bar
> > )
> > ```
> >
> > Thank you
> > --
> > Best regards,
> > Luigi
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
This essentially has transformed the stripplot into a boxplot... On Fri, Oct 25, 2019 at 11:19 AM PIKAL Petr <petr.pikal at precheza.cz> wrote:> > Hi > > I asked similar question few yeas ago (in different context) and besed on > answers I made custom function which adds line after the lattice graph is > plotted. > > after your lattice plot just do > > addLine(h=aggregate(df$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 > > > > > > ______________________________________________ > > > R-help at 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 at 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
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 > > > > > > > > ______________________________________________ > > > > R-help at 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 at 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