Creating contour or percentile lines in R

Question

I am creating the following contour graph from this matrix. I would like to, however, have also a plot which displays chosen by me contour lines (without filled contour) representing values of 0.50 (in black) and 0.25 and 0.75 (in red). Help on the method will be much appreciated.

B = matrix(c(0.158,0.182,0.306,0.46,0.601,0.77,0.796,0.832,
             0.174,0.216,0.373,0.58,0.769,0.862,0.907,0.929,
             0.164,0.262,0.442,0.73,0.886,0.93,0.949,0.976,
             0.171,0.218,0.509,0.791,0.915,0.972,0.987,0.992,
             0.174,0.288,0.563,0.848,0.961,0.993,0.998,1,
             0.185,0.288,0.618,0.89,0.976,0.993,0.996,1,
             0.215,0.317,0.667,0.911,0.988,0.999,0.999,0.999,
             0.199,0.328,0.685,0.957,0.994,1,1,1,
             0.231,0.362,0.741,0.953,0.998,1,1,1,
             0.237,0.373,0.782,0.976,0.999,1,1,1,
             0.25,0.398,0.799,0.974,0.997,1,1,1,
             0.26,0.443,0.855,0.989,0.999,1,1,1,
             0.272,0.478,0.868,0.994,1,1,1,1,
             0.256,0.487,0.91,0.996,1,1,1,1,
             0.268,0.508,0.933,1,1,1,1,1),
             nrow=15, ncol=8,byrow=T) 


# Change column names
nv <- c(20,30,40,50,60,70,80,90,100,110,120,140,160,180,200)
location <- c(0,1,2,3,4,5,6,7) 
rownames(B) <- nv
colnames(B) <- location


# Create levels so they can be uniform accross all the images
b <- seq(0,1,0.05)

# Make levels that cover both ranges of z values
lvls <- pretty(range(b),20)

# Set up axis labels
matrix.axes <- function(data) {
        # Do the rows, las=2 for text perpendicular to the axis
        x <- (1:dim(data)[1] - 1) / (dim(data)[1] - 1);
        axis(side=1, at=x, labels=rownames(data), las=2);
        # Do the columns
        x <- (1:dim(data)[2] - 1) / (dim(data)[2] - 1);
        axis(side=2, at=x, labels=colnames(data), las=2);
}


filled.contour(B, plot.axes=matrix.axes(B),
               plot.title=title(main=paste("Graph"),
                                xlab='Sample number',ylab='Distance'),
               color.palette=colorRampPalette(c('white','blue','yellow','red','darkred')),
               levels=lvls)

Filled contour above is what I have at the moment but want to change it to graph with distinct contour lines representing 0.50 (in black) and 0.25 and 0.75 (in red) values instead (3 lines total). I am tagging ggplot2 as there might be solution there?

why don't you just change the color in your colorRampPalette() expression? — MLavoie
– MLavoie, Commented Jan 12, 2016 at 10:59
Above is a surface plot where every value is represented by a colour. I want to change the graph to represent three thin lines each representing a distinct value. Does it make it more clear? — mihoo
– mihoo, Commented Jan 12, 2016 at 11:03
have you look into stat.ethz.ch/R-manual/R-devel/library/graphics/html/… ? — MLavoie
– MLavoie, Commented Jan 12, 2016 at 11:13

Axeman · Accepted Answer · 2016-01-12 11:23:17Z

1

Use the contour function instead:

contour(B, levels = c(0.25, 0.5, 0.75), col = c(2, 1, 2), axes = F,
        xlab = 'Sample number', ylab = 'Distance')
axis(1, at = seq(0, 1, length= length(nv)), labels = nv)
axis(2, at = seq(0, 1, length= length(location)), labels = location)

answered Jan 12, 2016 at 11:23

Axeman

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mihoo · Accepted Answer · 2016-01-12 11:20:35Z

0

I managed to solve it quite easily!

contour(B,levels=c(0.5),lwd=3)
contour(B,levels=c(0.25,0.75), lwd=2, col = 34, add=TRUE)

answered Jan 12, 2016 at 11:20

mihoo

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