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")$col[which.packet()])
},
# add median bar
)
```
Thank you
--
Best regards,
Luigi
Yes, it's possible to do about anything in lattice, but you have to learn
how to write custom panel functions, which takes some effort. If you want
to use lattice in this way, you should probably go through Deepayan's book.
Here is one way to do what I think you want. Note that it depends on
knowing that when the x axis is a factor, the x positions of the y
variables are at 1, 2, 3, .. etc (to the number of levels of the factor) to
draw the horizontal line segments. This is documented somewhere, but I
don't remember where.
stripplot(
Aboundance ~ Taxon|Group,
df,
groups = Taxon,
scales=list(y=list(log=T)),
pch=16, cex = 1.5,
ylab = expression(bold("Number of taxons")),
jitter.data = TRUE,
layout=c(3,1),
col = "black",
# colour panels differently
par.settings=list(strip.background=list(col=c("darkorchid3",
"darkolivegreen3",
"brown3"))),
strip = function(...,bg) {
strip.default(...,
bg
trellis.par.get("strip.background")$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")$col[which.packet()])
> },
> # add median bar
> )
> ```
>
> Thank you
> --
> Best regards,
> Luigi
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
Hi
I asked similar question few yeas ago (in different context) and besed on
answers I made custom function which adds line after the lattice graph is
plotted.
after your lattice plot just do
addLine(h=aggregate(df$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.