R help - Oct 2021 - How to add error bars to lattice xyplot

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.
What is the correct syntax? can I use raw data instead of making the
mean and std dev separately?
Thanks

-- 
Best regards,
Luigi

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
>
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