[R] How to add error bars to lattice xyplot

[Luigi Marongiu]

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