I have now been able to do what I believe you were aiming to do originally.

Firstly, you'll still require a further modified pairsKB function, again on my GitHub page. Only the following lines are now edited:

• 16-22 - to remove axis ticks and numbers (you may want these, in which case set labels=TRUE, tick=TRUE
• 147-151 - to pass an index value to the diagonal function

-----------------------

I also further edited your other functions (not all):

panel.smooth.ordered.categorical <- function (x, y, col = par("col"), bg = NA, pch = par("pch"), cex = 1, col.smooth = "red", span = 2/3, iter = 3,point.size.rescale = 1.0, ...)
{ 
    ################################################
    #Edited next line, 27th November 2017 by Kevin Blighe
    #A vector to be used for colouring the dots
    ################################################
    dotColours <- c(rep("royalblue", 2), rep("black", 2), rep("forestgreen", 2))

    require(reshape2)

    z <- merge(data.frame(x,y), melt(table(x ,y)),sort =F)$value

    z <- point.size.rescale*z/ (length(x))

    symbols( x, y, circles = z,
        #rep(0.1, length(x)),
        #sample(1:2, length(x), replace = T),

        ################################################
        #Edited next line, 27th November 2017 by Kevin Blighe
        #Supply the dotColours vector, and setting dot border to black
        ################################################
        inches=F, bg=dotColours, fg="black", add = T)

    #points(x, y, pch = pch, col = col, bg = bg, cex = cex)

    ok <- is.finite(x) & is.finite(y)

    if (any(ok))
        lines(stats::lowess(x[ok], y[ok], f = span, iter = iter), col = col.smooth, ...)
}

To suit the colour designations for the points, you'll have to set the dotColours vector manually, eg: dotColours <- c(rep("royalblue", 4), rep("black", 4), rep("forestgreen", 4), ...), for first 4 values in one colour, 5-8 in another, et cetera.

-----------------------

################################################
#Edited next line, 27th November 2017 by Kevin Blighe
#Modified standard panel.hist function to additionally accept column index being plotted
################################################
panel.hist <- function(x, i, ...)
{
    usr <- par("usr"); on.exit(par(usr))
    par(usr = c(usr[1:2], 0, 1.5) )
    h <- hist(x, plot = FALSE)
    breaks <- h$breaks; nB <- length(breaks)
    y <- h$counts; y <- y/max(y)

    ################################################
    #Edited next 4 lines, 27th November 2017 by Kevin Blighe
    #Now colouring each histogram based on WGCNA module names
    ################################################
    if ( is.na(colnames(MEs)[i]) )
        rect(breaks[-nB], 0, breaks[-1], y, col="white", ...)
    else
        rect(breaks[-nB], 0, breaks[-1], y, col=colnames(MEs)[i], ...)
}

Set the value of the histograms where there's no colour to be used to "white" (you can change this to anything), otherwise, set the colour as the name of the WGCNA module

-----------------------

pairs.ordered.categorical <- function(xx,...) 
{
    ################################################
    #Edited next line, 27th November 2017 by Kevin Blighe
    #Now invoking pairsKB, not pairs
    ################################################
    pairsKB(xx, diag.panel=panel.hist, lower.panel=panel.smooth.ordered.categorical, upper.panel=panel.cor.ordered.categorical, cex.labels=0.8,...)
}

Invokes my pairsKB function to get the histogram colouring correct,

-----------------------

traits_needed <-c("blade_Na","sheath_Na","blade_K","sheath_K","blade_K_Na")
needed <- c("darkgoldenrod4","darkseagreen3","brown3","palevioletred3","darkolivegreen")
pairs.ordered.categorical(cbind(MEs[, needed], traitsDat[, traits_needed]))

The colouring of the histograms will only work if MEs are positioned first in your object, but I think that's the way that you want.

There are undoubtedly more ways of doing this. The pairs function is quite powerful if one can grasp how it works. I devoted a full day to understanding its code, going line by line.

Kevin

Ah, I do apologise (I'm British - we apologise for everything), it was actually a formatting issue with how the system on Biostars interprets code. There's a glitch whereby a parenthesis can 'vanish'.

I have edited the code again. It was just the line if ( is.na(colnames(MEs)[i]) ) in the hist function.

I would also just be wary of the colour vector in panel.smooth.ordered.categorical. I'm just trying to double confirm that the symbols function does actually colour the dots in the order they appear in the data (one would expect that they do).