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R Lattice Dotplot Error Bars


Bunker <[hidden email]> wrote: >> Dear R users, >> >> About a year ago Deepayan offered a suggestion to incorporate error bars >> into a dotplot using the singer data as To accomplish this we're going to need to define our own panel function. To better see all the factors you want to plot, I would first make lines connections between your groups, to better see individual effects within different sample.size. panel.xyplot(x, y, pch=16, cex=1.2, col='white') I then superimpose on top of them a slightly smaller open circle with a black border. http://johnlautner.net/error-bars/r-lattice-error-bars.html

It probably would have made more sense to have made hormone treatment = normal the reference group because it serves as the control in this experiment. Thanks, Dan prepanel.ci <- function(x, y, lx, ux, subscripts, ...) { x <- as.numeric(x) lx <- as.numeric(lx[subscripts]) ux <- Colin Wahl Threaded Open this post in threaded view ♦ ♦ | Report Content as Inappropriate ♦ ♦ Re: dotplots with error bars In reply to this post by Jim If you want to use default settings for the axis just enter the number and nothing more.

Dot Plot With Error Bars In R

If you want additional features beyond the default you will need to construct your own panel function. Thanks. –PaoloCrosetto Nov 25 '13 at 19:46 I ended up using yur code (and learning a lot about ggplot2). Each panel graphing function adds a specific feature to the graph. Is it possible somehow?

Probability smear graphs ANOVA models are regression models in which all the regressors are dummy variables. plot(range(new.data[,2:6]), c(1-.3,7+.3), type='n', xlab='Effect estimates', ylab='', axes=F) In the first argument I use the range function to return the minimum and maximum x-limits (using the numerical columns of the data frame). Idiomatic Expression that basically says "What's bad for you is good for me" Shh! Geom_dotplot I thought of "up=z+se, lo=z-se, panel.groups=function(x,y,..., up, lo, subscripts){ up <- up[subscripts]; lo <- lo[subscripts]; panel.segments(lo, as.numeric(y), up, as.numeric(y), ...)}", but that doesn't seem to work.

This implies that the diet × Ru486 effect is no larger than effects attributable to ordinary background genetic variation. The effect of the different levels of a grouping variable is displayed in the same panel unlike the conditioning variable whose effect is displayed across panels. Fig. 17A lattice plot that used a loop to draw the separate groups Cited references Donahue, R. https://www.unc.edu/courses/2010fall/ecol/563/001/docs/lectures/lecture5.htm I take the various panel functions from the previous section and remove the lead word "panel.".

Binary to decimal converter What is a good antonym for "commiserate"? Lattice R I presume this is a technicality due to the a numeric >> variable being identified as a factor. par(mfrow=c(1,2)) plot(c(.8,3.2), range(fac.vals[,c("up95", "low95")]), type='n', xlab="Hormonal treatment", ylab='Estimated mean', axes=F) axis(1, at=1:3, labels=levels(fac.vals$fac1)) axis(2) box() dat1 <- fac.vals[fac.vals$fac3==1,] #first food group cur.dat <- dat1[dat1$fac2=='D',] #amount of shift myjitter <- -.05 arrows(cur.dat$fac1.num+myjitter, One solution to this is Sundar's > approach, which is to change the panel function to handle groups. > Another generic solution is to use 'panel.superpose', which _does_ > know how

R Dotchart

I have two questions. I need to order my groups into meaningful groups to properly display my data. Dot Plot With Error Bars In R xyplot(est~fac1|factor(fac3), groups=fac2, data=fac.vals, type='b', col=c(1,2), pch=c(16,1), ylim=range(fac.vals[,'low95']-.1, fac.vals[,'up95']+.1), panel.groups="my.panel", panel="panel.superpose") Fig. 15A lattice plot using the group.number variable Finally I fix the labels on the x-axis, y-axis, and in the panels Dot Plot Ggplot2 lines(cur.dat$fac1.num+myjitter, cur.dat$est, col=1) points(cur.dat$fac1.num+myjitter, cur.dat$est, col=1, pch=16) I next repeat these same lines of code for the second diet, fac2 = 'S', with the following changes.

For instance corner(0,0) denotes the bottom left corner while corner(1,1) specifies the top right corner. navigate here useOuterStrips(dotplot(z ~ factor(sample.size) | as.factor(effect.size)*as.factor(true.dose), groups=as.factor(type), data=df.dose, as.table=TRUE, horizontal=FALSE, jitter.x=TRUE)) To add an error bar, it's a little more complicated because you have groups within the panels, so you need to The last one is a relatively new R package that is based on Leland Wilkinson's (of SYSTAT fame) "grammar of graphics". The hormone treatment yields the biggest change in the response with normal and Ru486 yielding roughly the same effect relative to the reference group corticosterone. Ggplot Error Bars

I'm afraid I have not (YET) managed to understand just how Lattice works. When the panel function is called upon to draw a panel the variable subscripts contains the value of fac3 (the variable that defines the panels) for the current panel. lower95<-ests+qnorm(.025)*std.errs upper95<-ests+qnorm(.975)*std.errs lower50<-ests+qnorm(.25)*std.errs upper50<-ests+qnorm(.75)*std.errs Finally I assemble everything in a data frame. http://johnlautner.net/error-bars/r-lattice-xyplot-error-bars.html I searched far and wide >> and cannot find a suitable option. >> >> I am trying to produce publication-quality figures for my thesis >> results.

The panel.superpose function in turn calls something called a panel.groups function that by default is panel.xyplot in which the points are colored separately by group. The cex.axis=.8 option reduces the size of the labels to 80% of the default size. Deepayan Sarkar Threaded Open this post in threaded view ♦ ♦ | Report Content as Inappropriate ♦ ♦ Re: [R] adding error bars to lattice plots On 10/13/06, Daniel E.

This is also the role the notation x and y have in the function.

See my edit. –Aaron Oct 11 '12 at 15:53 Yes, now it looks as it should be. The argument groups=fac2 generates the two profiles that appear within each panel differentiated by color. legend('topleft', c('Detritus','Shrimp'), col=1:2, pch=c(16,1), cex=.8, pt.cex=.9, title=expression(bold('Food Type')),bty='n') The first argument of legend is the location of the legend in the plot. arrows(cur.dat$fac1.num+myjitter, cur.dat$low95, cur.dat$fac1.num+myjitter, cur.dat$up95, angle=90, code=3, length=.05, col=1) I follow this up with the lines function to draw the mean profile and the points function to plot the estimates at the

I thought of "geom_segment(aes(x=sample.size, xend=sample.size, y=z-100, yend=z+100))", but that doesn't seem to work with the facet grid. Please try the request again. In this case we want to generate mean profile plots separately for the levels of a third variable fac3 (sibship type). http://johnlautner.net/error-bars/r-error-bars.html I use a positive value of myjitter so that the points and error bars are moved slightly to the right.

For these data grpvals = c('D', "S") and has the same value for both panels.. I did find a function "dotplots.errors" available here: http://agrobiol.sggw.waw.pl/~cbcs/articles/CBCS_5_2_2.pdf. However, I have found this function absurdly difficult to use when customizing figures (ordering displays properly, or just simple getting the function to work.) I've been struggling for the last few