Your panel function needs to plot the points! See at ############ below
xyplot(Value ~ Concentration,
group = Substance, data = df,
pch = 16, cex = 1.2, type = "b",
xlab=expression(bold(paste("Concentration (", mu,
"M)"))),
ylab=expression(bold("Infection rate")),
col=COLS,
scales = list(x = list(log = 10, at=c(unique(df$Concentration))
)
),
key = list(space="top", columns=4, col = "black",
points=list(pch=c(16, 16, 16, 16),
col=COLS
),
text=list(c("A", "B", "C",
"D")
)
),
panel = function (x,y,...) {
panel.xyplot(x,y, ...) ###########
panel.segments(x0 = log10(df$Concentration),
x1 = log10(df$Concentration),
y0 = df$Value - dfsd$Value,
y1 = df$Value + dfsd$Value,
col = COLS)
}
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Mon, Oct 11, 2021 at 12:24 PM Luigi Marongiu <marongiu.luigi at
gmail.com>
wrote:
> Thanks,
> now I got the bars (although without notch) but I lost the main plot:
> ```
> xyplot(Value ~ Concentration,
> group = Substance, data = df,
> pch = 16, cex = 1.2, type = "b",
> xlab=expression(bold(paste("Concentration (", mu,
"M)"))),
> ylab=expression(bold("Infection rate")),
> col=COLS,
> scales = list(x = list(log = 10, at=c(unique(df$Concentration))
> )
> ),
> key = list(space="top", columns=4, col = "black",
> points=list(pch=c(16, 16, 16, 16),
> col=COLS
> ),
> text=list(c("A", "B", "C", "D")
> )
> ),
> panel = function (x,y) {
> panel.segments(x0 = log10(df$Concentration),
> x1 = log10(df$Concentration),
> y0 = df$Value - dfsd$Value,
> y1 = df$Value + dfsd$Value,
> col = COLS)
> }
>
> )
> ```
> I will check xYplot out, I think it is the tool for the job.
>
> On Mon, Oct 11, 2021 at 3:56 PM Deepayan Sarkar
> <deepayan.sarkar at gmail.com> wrote:
> >
> > On Mon, Oct 11, 2021 at 5:41 PM Luigi Marongiu <marongiu.luigi at
gmail.com>
> wrote:
> > >
> > > Hello,
> > > I am trying to plot data using lattice. The basic plot works:
> > > ```
> > > Substance = rep(c("A", "B", "C",
"D"),4)
> > > Concentration = rep(1:4,4),
> > > Value = c(62.80666667, 116.26333333, 92.26000000, 9.87333333,
> 14.82333333,
> > > 92.37333333, 98.95666667, 1.48333333, 0.64666667,
> 50.66000000,
> > > 25.75333333, 0.69000000, 0.21666667, 7.40666667,
> 6.92000000,
> > > 0.06333333)
> > > df = data.frame(Substance, Concentration, Value, stringsAsFactors
> FALSE)
> > > Value = c(15.2974126, 16.3196089, 57.4294280, 9.1943370,
20.5567321,
> > > 14.0874424,
> > > 38.3626672, 0.3780653, 0.4738495, 37.9124874, 16.2473916,
> 0.7218726,
> > > 0.2498666, 8.4537585, 10.8058456, 0.1096966)
> > > dfsd = data.frame(Substance, Concentration, Value,
stringsAsFactors > FALSE)
> > >
> > > library(lattice)
> > > COLS = c("gold", "forestgreen",
"darkslategray3", "purple")
> > > xyplot(Value ~ Concentration,
> > > group = Substance, data = df,
> > > pch = 16, cex = 1.2, type = "b",
> > > xlab=expression(bold(paste("Concentration (",
mu, "M)"))),
> > > ylab=expression(bold("Infection rate")),
> > > col=COLS,
> > > scales = list(x = list(log = 10,
at=c(unique(df$Concentration))
> > > )
> > > ),
> > > key = list(space="top", columns=4, col =
"black",
> > > points=list(pch=c(16, 16, 16, 16),
> > > col=COLS,
> > > text=list(c("6-PN",
"8-PN", "IX", "XN")
> > > )
> > > )
> > > )
> > >
> > > )
> > > ```
> > > but how do I add the error bars?
> > > I tried with
> > > ```
> > > xyplot(Value ~ Concentration,
> > > group = Substance, data = df,
> > > pch = 16, cex = 1.2, type = "b",
> > > xlab=expression(bold(paste("Concentration (",
mu, "M)"))),
> > > ylab=expression(bold("Infection rate")),
> > > col=COLS,
> > > scales = list(x = list(log = 10,
at=c(unique(df$Concentration))
> > > )
> > > ),
> > > key = list(space="top", columns=4, col =
"black",
> > > points=list(pch=c(16, 16, 16, 16),
> > > col=COLS,
> > > text=list(c("6-PN",
"8-PN", "IX", "XN")
> > > )
> > > )
> > > ),
> > > panel = function (x,y,) {
> > > panel.segments(x0 = df$Concentration, x1 =
df$Concentration,
> > > y0 = df$Value - dfsd$Value,
> > > y1 = df$Value + dfsd$Value,
> > > col = COLS)
> > > }
> > >
> > > )
> > > ```
> > > but the bars are plotted outside the graph.
> >
> > You need to apply the log-transformation yourself, e.g.,
> >
> > panel.segments(x0 = log10(df$Concentration), x1 > >
log10(df$Concentration),
> >
> > But this is not really a scalable approach. You should check if
> > Hmisc::xYplot suits your needs:
> >
> > https://search.r-project.org/CRAN/refmans/Hmisc/html/xYplot.html
> >
> > Best,
> > -Deepayan
> >
> > > What is the correct syntax? can I use raw data instead of making
the
> > > mean and std dev separately?
> > > Thanks
> > >
> > > --
> > > 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.
>
>
>
> --
> 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.
>
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