On Mon, Oct 11, 2021 at 5:41 PM Luigi Marongiu <marongiu.lu...@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@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. ______________________________________________ R-help@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.