[R] cluster data in lattice dotplot and show stdev

[Duncan Mackay]

Hi Luigi

I think your data is duplicated

> xtabs(~cluster+type+target,my.data)
, , target = A

       type
cluster blank negative positive
  run_1     2        2        2
  run_2     0        0        0

, , target = B

       type
cluster blank negative positive
  run_1     0        0        0
  run_2     2        2        2

> xtabs(~cluster+target,my.data)
       target
cluster A B
  run_1 6 0
  run_2 0 6

I am not sure exactly what you want partly because what Jim has plotted.
I have thought of 2 ways. I have added columns coding the factors as numeric
to make it flexible

1. By runs
my.data$Target <- paste0(rep(LETTERS[1:2],each= 6),rep(1:2,each=3))
my.data$x <- rep(c(0.8,1.2),each=3)
my.data$xrun <- rep(1:3)

xyplot(value ~ x|target,my.data,
       groups = type,
       xlim = c(0.5,1.5),
       scales = list(x = list(at= c(0.8,1.2),
                     label=paste("Run",1:2)),
                     alternating = 1),
       auto.key = list(points = T,
                       lines = F),
       pch=16,
       panel = panel.superpose,
       panel.groups = function(x,y,...){
       
                        panel.xyplot(x,y, ...)
                        
       
               }
)

2. By type

xyplot(value ~ xrun|target,my.data,
       groups = run,
       xlim = c(0,4),       
      par.settings = list(strip.background = list(col = "transparent")),
       scales = list(x = list(at= c(1:3),
                     label= unique(my.data$type),
                     alternating = 1)),
       auto.key = list(points = T,
                       lines = F),
       pch=16,
       panel = panel.superpose,
       panel.groups = function(x,y,...){

                        panel.xyplot(x,y, ...)


               }
)

If you want error bars use the functions in 
demo(lattice::intervals)
or use your own panel .segments

If you decide not to use default colours etc use 

panel.settings = list(superpose.symbol = list(pch = ... ,
                                              col = ... ,
                                              cex = 1))

makes keys easier
                                                    
example by hand error bars

xyplot(value ~ xrun|target,my.data,
       groups = run,
       xlim = c(0,4),
       par.settings = list(strip.background = list(col = "transparent"),
                                          grid.pars = list(lineend =
"butt")),
       scales = list(x = list(at= c(1:3),
                     label= unique(my.data$type),
                     alternating = 1)),
       auto.key = list(points = T,
                       lines = F),
       pch=16,
       panel = panel.superpose,
       panel.groups = function(x,y,...,group.number){

                        panel.xyplot(x,y, ...)

                        panel.arrows(group.number+0.3, group.number-0.6,
group.number+0.3, group.number-0.4,
                              length = 0.04,
                              unit = "inches",
                              angle = 90,
                              code = 3)

               }
)

Regards

Duncan

Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Luigi
Marongiu
Sent: Friday, 17 February 2017 02:31
To: r-help
Subject: [R] cluster data in lattice dotplot and show stdev

dear all,
i have a set of data that is separated in the variables: cluster (two
runs), type (blank, negative and positive) and target (A and B), each
duplicated. I am plotting it with lattice and the result is a 2x2 matrix
plot in which the top two cells (or panels) are relative to run 2, the
lower to run 2; each panel is then subdivided in target A or B and I have
colour-coded the dots to match the target.
However i would like to have a 1x2 panel plot representing the targets, and
within each panel having a cluster of 3 dots (representing the types) for
run 1 and another for run 2. I tried to represent such requirement in the
rough construction at the end of the example.
also, since each run is actually formed by duplicates, each dot should
indicate the standard deviation of the values.
How would I do that? any tips?
thanks
luigi

>>>
cluster <- c(rep("run_1", 6), rep("run_2", 6))
type <- rep(c("blank", "positive", "negative"),2)
target <- c(rep("A", 6), rep("B", 6))
value <- c(0.01, 1.1, 0.5,
           0.02, 1.6, 0.8,
           0.07, 1.4, 0.7,
           0.03, 1.4, 0.4)
my.data <- data.frame(cluster, type, target, value)

library(lattice)
dotplot(
  value ~ type|cluster + target,
  my.data,
  groups = type,
  pch=21,
  main = "Luminex analysis MTb humans",
  xlab = "Target", ylab = "Reading",
  col = c("grey", "green", "red"),
  par.settings = list(strip.background = list(col="paleturquoise")),
  scales = list(alternating = FALSE, x = list(labels = c("", "", ""))),
  key = list(
    space = "top",
    columns = 3,
    text = list(c("Blank", "Negative", "Positive"), col="black"),
    rectangles = list(col=c("grey", "green", "red"))
  )
)

x <- 1:7
plot(x , c(max(my.data$value), min(my.data$value), my.data$value[1:5]),
col="white", xaxt = "n", ylab="value", xlab="target")
points(x[1], mean(my.data$value[1], my.data$value[4]), col="grey")
points(x[2], mean(my.data$value[2], my.data$value[5]), col="red")
points(x[3], mean(my.data$value[3], my.data$value[6]), col="green")
points(x[5], mean(my.data$value[7], my.data$value[10]), col="grey")
points(x[6], mean(my.data$value[8], my.data$value[11]), col="red")
points(x[7], mean(my.data$value[9], my.data$value[12]), col="green")
axis(side=1, at = x[2], lab = "A", cex.axis=1)
axis(side=1, at = x[6], lab = "B", cex.axis=1)

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