Luigi Marongiu
2020-Sep-25 11:53 UTC
[R] package plotrix: how to account for two two z categories
Thanks! looks nicer already. I am attaching the figure I temporarily made with normal brkdn.plot but yours has more information. Best regards Luigi On Fri, Sep 25, 2020 at 1:43 PM Jim Lemon <drjimlemon at gmail.com> wrote:> > Hi Luigi, > Here is a quick example of how points would look in the same > configuration. Perhaps with end caps to show the nesting it may be > more like what you want. > > Jim > > On Thu, Sep 24, 2020 at 6:34 PM Jim Lemon <drjimlemon at gmail.com> wrote: > > > > Oh, sorry, forgot about the colors. A list beginning with the color > > for the overall summary, then colors for the first factor and so on. > > See the help page for examples. > > > > Jim > > > > On Thu, Sep 24, 2020 at 6:32 PM Jim Lemon <drjimlemon at gmail.com> wrote: > > > > > > Hi Luigi, > > > I thought a lot about that when I was writing the function. The only > > > way I could think of to show the nesting was dots with horizontal > > > lines and it looked messy and was quite hard to visualize the nesting. > > > If you do have any great ideas I always welcome contributions to > > > plotrix. > > > > > > Jim > > > > > > On Thu, Sep 24, 2020 at 6:25 PM Luigi Marongiu <marongiu.luigi at gmail.com> wrote: > > > > > > > > Thank you Jim, that is really nice! > > > > But is there a way to use dots instead of boxes? and how do I control > > > > the colours? > > > > Best regards > > > > Luigi > > > > > > > > On Thu, Sep 24, 2020 at 9:29 AM Jim Lemon <drjimlemon at gmail.com> wrote: > > > > > > > > > > Hi Luigi, > > > > > To display a nested breakdown like this I would suggest barNest. This > > > > > is one way to display the nesting. Note that if you change the order > > > > > of the factors in the formula you will get a different plot, so think > > > > > about how you want the summaries nested. Error bars can only be > > > > > displayed on the final breakdown. > > > > > > > > > > # because you have fairly long labels, use a wide plot > > > > > x11(width=10) > > > > > barcol<-list("lightgray",c("#ff00ff","#ff99ff"), > > > > > c("#00ff00","#66ff66"),c("#aaaa00","#888800")) > > > > > barNest(y~x+z+w,Q,main="Double Measurement", > > > > > ylab="Response",col=barcol,errbars=TRUE) > > > > > > > > > > Jim > > > > > > > > > > On Wed, Sep 23, 2020 at 10:48 PM Luigi Marongiu > > > > > <marongiu.luigi at gmail.com> wrote: > > > > > > > > > > > > Hello, > > > > > > I have an experiment measuring optical density (OD) when comparing > > > > > > three parameters: > > > > > > a) concentration of the target > > > > > > b) concentration of the probe > > > > > > c) concentration of the reporter antibody. > > > > > > Using plotrix I can nicely draw the first two into clusters, but I > > > > > > can't get separation for the third parameter. is there a way in > > > > > > plotrix to custer data according to two, let's say, z parameters (I > > > > > > call the second high-level parameter as w)? For instance, two > > > > > > clusters, each separated into two subclusters. Or is this more a job > > > > > > for lattice? > > > > > > Thank you. > > > > > > > > > > > > ``` > > > > > > x = rep(c(rep("1000 pmol", 4), rep("0 pmol", 4)),2) > > > > > > z = rep(c(rep("Treated", 2), rep("Untreated", 2), rep("Treated", 2), > > > > > > rep("Untreated", 2))) > > > > > > w = c(rep("1:1000", 8), rep("1:2000", 8)) > > > > > > y = c(1.18, 1.22, 1.52, 2.37, 0.97, 1.08, 1.17, 1.58, 1.16, 1.16, 2.27, 2.24, > > > > > > 1.26, 1.28, 1.39, 1.77) > > > > > > Q = data.frame(x, z, w, y, stringsAsFactors = FALSE) > > > > > > names(Q) = c("[Target]", "Enzyme", "[Antibody]", "OD") > > > > > > names(Q) = c("x", "z", "w", "y") # for ease, I'll use single letters > > > > > > library(plotrix) > > > > > > brkdn.plot(y~x+z, data=Q, > > > > > > pch = c(1, 16), cex = 1.5, type="p", > > > > > > main="Single Measurement", > > > > > > xlab=expression(bold("S1 nuclease")), > > > > > > ylab=expression(bold("Optical density"))) > > > > > > brkdn.plot(y~x+z+w, data=Q, > > > > > > pch = c(1, 16), cex = 1.5, type="p", > > > > > > main="Double Measurement", > > > > > > xlab=expression(bold("S1 nuclease")), > > > > > > ylab=expression(bold("Optical density"))) > > > > > > ``` > > > > > > > > > > > > ______________________________________________ > > > > > > R-help at 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-- Best regards, Luigi -------------- next part -------------- A non-text attachment was scrubbed... Name: Rplot.png Type: image/png Size: 10203 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20200925/63705b08/attachment.png>
Jim Lemon
2020-Sep-25 22:20 UTC
[R] package plotrix: how to account for two two z categories
Hi Luigi,
Good illustration. Maybe if I can integrate vertical lines to show the
nesting instead of bars it would work better. While it makes the
nesting much clearer, some people may still accuse you of using a bar
plot.
# new functions with the modifications
source("barNest.R")
source("drawNestedSpans.R")
png("lm_plot.png",width=600)
barNest(y~w+z+x,Q,main="Double Measurement",
ylab="Response",col=barcol,errbars=TRUE)
dev.off()
Jim
On Fri, Sep 25, 2020 at 9:54 PM Luigi Marongiu <marongiu.luigi at
gmail.com> wrote:>
> Thanks! looks nicer already.
> I am attaching the figure I temporarily made with normal brkdn.plot
> but yours has more information.
> Best regards
> Luigi
>
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Jim Lemon
2020-Sep-25 22:51 UTC
[R] package plotrix: how to account for two two z categories
Hmmm, maybe without the caps... Jim On Sat, Sep 26, 2020 at 8:20 AM Jim Lemon <drjimlemon at gmail.com> wrote:> > Hi Luigi, > Good illustration. Maybe if I can integrate vertical lines to show the > nesting instead of bars it would work better. While it makes the > nesting much clearer, some people may still accuse you of using a bar > plot. > > # new functions with the modifications > source("barNest.R") > source("drawNestedSpans.R") > png("lm_plot.png",width=600) > barNest(y~w+z+x,Q,main="Double Measurement", > ylab="Response",col=barcol,errbars=TRUE) > dev.off() > > > Jim > > On Fri, Sep 25, 2020 at 9:54 PM Luigi Marongiu <marongiu.luigi at gmail.com> wrote: > > > > Thanks! looks nicer already. > > I am attaching the figure I temporarily made with normal brkdn.plot > > but yours has more information. > > Best regards > > Luigi > >-------------- next part -------------- A non-text attachment was scrubbed... Name: lm_plot.png Type: image/png Size: 18859 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20200926/bcaaf4e8/attachment.png>