[R] How to add error bars to lattice xyplot

[Bert Gunter]

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 using 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$Value,
> col = COLS)
> }
>
> )
> ```
> I will check xYplot out, I think it is the tool for the job.
>
> On Mon, Oct 11, 2021 at 3:56 PM Deepayan Sarkar
> <deepayan.sarkar using gmail.com> wrote:
> >
> > On Mon, Oct 11, 2021 at 5:41 PM Luigi Marongiu <marongiu.luigi using gmail.com>
> wrote:
> > >
> > > Hello,
> > > I am trying to plot data using lattice. The basic plot works:
> > > ```
> > > Substance = rep(c("A", "B", "C", "D"),4)
> > > Concentration = rep(1:4,4),
> > > Value = c(62.80666667, 116.26333333,  92.26000000,   9.87333333,
> 14.82333333,
> > >           92.37333333, 98.95666667,   1.48333333,   0.64666667,
> 50.66000000,
> > >           25.75333333,   0.69000000, 0.21666667,   7.40666667,
>  6.92000000,
> > >           0.06333333)
> > > df = data.frame(Substance, Concentration, Value, stringsAsFactors =
> FALSE)
> > > Value = c(15.2974126, 16.3196089, 57.4294280,  9.1943370, 20.5567321,
> > > 14.0874424,
> > >        38.3626672, 0.3780653,  0.4738495, 37.9124874, 16.2473916,
> 0.7218726,
> > >        0.2498666,  8.4537585, 10.8058456,  0.1096966)
> > > dfsd = data.frame(Substance, Concentration, Value, stringsAsFactors =
> FALSE)
> > >
> > > library(lattice)
> > > COLS = c("gold", "forestgreen", "darkslategray3", "purple")
> > > xyplot(Value ~ Concentration,
> > >        group = Substance, data = df,
> > >        pch = 16, cex = 1.2, type = "b",
> > >        xlab=expression(bold(paste("Concentration (", mu, "M)"))),
> > >        ylab=expression(bold("Infection rate")),
> > >        col=COLS,
> > >        scales = list(x = list(log = 10, at=c(unique(df$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 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
>
> ______________________________________________
> 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.
>

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