Custom legend R plots (Lattice)

Question

I am trying to add a custom legend to a lattice plot but I can't make as I want. Below is my code. I want to make a legend for a lattice plot that looks like the one created using mtext() but with the symbols I used using legend. It would be great if I could make the male and female symbols darker or with different colors. Thank you.

plot.new()
legend("bottom", legend = c("\u2640 12h Ant", "\u2640 4d Ant", "\u2640 3h Ant",
                            "\u2640 24h Ant", "\u2640 48h Ant", "\u2640 72h Ant", "\u2640 4d HT",
                            "\u2640 3h HT", "\u2640 24h HT", "\u2640 48h HT", "\u2640 72h HT",
                            "\u2642 4d Ant", "\u2642 4d HT"),
       bty = "n",
       xjust = 0,
       ncol = 7,
       lwd = 2, cex = 0.8,
       col = c("red","blue","green","pink","maroon4",
               "cyan3","blue","green","pink","maroon4","cyan3", "blue", "blue"),
       lty = c(NA, NA, NA),
       pch = c(15,15,15,15,15,15,19,19,19,19,19,17,2))


#I want to make one legend like this, but mtext cannot add symbols :(
mtext("Antennae:
       \u2640  12h  4d  3h  24h  48h  72h  \u2642 4d
       Head+Thorax:
      \u2640  12h  4d  3h  24h  48h  72h  \u2642 4d
      ", side = 1, padj=1, adj=0, line=FALSE, outer=FALSE)

Here is my current plot, I want to change the legend to include male and female symbols

Update: Here a small data set data

Here is the R code to generate the Trellis graph:

#Command to load packages, not all needed
library("RColorBrewer")
library("gplots")
library("plyr")
library("lattice")
library("Hmisc")
library("latticeExtra")
library("scatterplot3d")
library("plotrix")
library("scales")

#Command clears the console
rm(list=ls())
#Command sets the working directory
setwd("/set-your-path-here")
miRs<-read.table("stackoverflow.csv", header=TRUE, sep=",")
attach(miRs)
head(miRs)
miRs.st<-stack(miRs[,2:14])
head(miRs.st)
miRs.st[,"miRs"]<-miRs[,1]
head(miRs.st)
summary(miRs.st$ind)
miRs.st$ind<-factor(miRs.st$ind, levels=c("Fem12hAnt", "Fem4dAnt", "Fem3hAnt",
                                          "Fem24hAnt", "Fem48hAnt", "Fem72hAnt", "Fem4dHT",
                                          "Fem3hHT", "Fem24hHT", "Fem48hHT", "Fem72hHT",
                                          "Male4dAnt", "Male4dHT"))

#create list of symbols to use in the legend
supsym <- trellis.par.get("superpose.symbol")
supsym$col <- c("red","blue","green","pink","maroon4","cyan3","blue","green","pink","maroon4","cyan3", "blue", "blue")
supsym$fill <- c("red","blue","green","pink","maroon4","cyan3","blue","green","pink","maroon4","cyan3", "blue", "blue") 
supsym$pch <- c(15,15,15,15,15,15,19,19,19,19,19,17,2)
supsym$cex <- c(.5,.5,.5,.5,.5,.5,.5,.5,.5,.5,.5,.5,.5) # otherwise symbol 15 appears a bit larger
trellis.par.set("superpose.symbol",supsym)

#set log scales in the axis
options(scipen=10)
options(digits=10)

#set background color to each gene, can change the color of those genes of interest
bgColors <- c("gray44", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44",
              "red", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44",
              "gray44", "gray80", "gray44", "gray80", "gray44")

#color of the text in the plot
txtColors <- c("white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white",
               "white", "black", "white", "black", "white")

# Create a function to be passes to "strip=" argument of xyplot
myStripStyle <- function(which.panel, factor.levels, ...) {
  panel.rect(0, 0, 1, 1,
             col = bgColors[which.panel],
             border = 1)
  panel.text(x = 0.5, y = 0.5,
             font=2,
             lab = factor.levels[which.panel],
             col = txtColors[which.panel])
}       

#plot the trellis graph
print(xyplot(values~ind|miRs,groups=ind,data=miRs.st,
             layout=c(5,5),as.table=TRUE,
             type="p",
             par.strip.text=list(custBgCol=bgColors,
                                 custTxtCol=txtColors),
             strip=myStripStyle,
             auto.key=list(space="bottom",columns=5, pch=8, cex=.8),
             relation="same",
             scales = list(x = list(draw = FALSE), y = list(log = 10)),
             yscale.components = yscale.components.log10ticks,
             main="miRs Expression",
             xlab="",
             ylab=expression('Number of Reads')))

Answer 1

I had some in-person discussion with the question author, who I think will be satisfied by a legend implemented in lattice instead of base, which simply requires a modification of the auto.key argument to the call to xyplot() Using the same code as above, try this call to xyplot(), specifying the legend text directly in the auto.key argument: text=c("\u2640 12h Ant", "\u2640 4d Ant", "\u2640 3h Ant", "\u2640 24h Ant", "\u2640 48h Ant", "\u2640 72h Ant", "\u2640 4d HT", "\u2640 3h HT", "\u2640 24h HT", "\u2640 48h HT", "\u2640 72h HT", "\u2642 4d Ant", "\u2642 4d HT"):

print(xyplot(values~ind|miRs, groups=ind, data=miRs.st, 
         layout=c(5,5), as.table=TRUE, type="p", 
         par.strip.text=list(custBgCol=bgColors, custTxtCol=txtColors), 
         strip=myStripStyle, 
         auto.key=list(text=c("\u2640 12h Ant", "\u2640 4d Ant", "\u2640 3h Ant", "\u2640 24h Ant", "\u2640 48h Ant", "\u2640 72h Ant", "\u2640 4d HT", "\u2640 3h HT", "\u2640 24h HT", "\u2640 48h HT", "\u2640 72h HT", "\u2642 4d Ant", "\u2642 4d HT"), space="bottom", columns=5, pch=8, cex=.8),
         relation="same",
         scales = list(x = list(draw = FALSE), y = list(log = 10)),
         yscale.components = yscale.components.log10ticks,
         main="miRs Expression",
         xlab="",
         ylab=expression('Number of Reads')))

Answer 2

MrFlick's question is as yet unanswered so I am going to proceed on the assumption that you actually wanted a base-graphics solution. The text function can plot outside the user-coordinate frame if the par-parameter "xpd" is set to TRUE, either in a par call or in the text call itself. The locator function returns an x-y value after first clicking once on hte plot window to change the focus and then again at the center of where you want this extra legend/annotation:

 text(locator(1), "Antennae:
        \u2640  12h  4d  3h  24h  48h  72h  \u2642 4d
        Head+Thorax:
       \u2640  12h  4d  3h  24h  48h  72h  \u2642 4d
       ", xpd=TRUE)

At the moment the request is too regarding location (which is why I gave the locator() option. It's also possible to use Hershey fonts using it's astrological symbols where the male is "Mars" and female is "Venus"