Colors to Plotting PCA (2D) by R

Question

[hosin]

Hi there

I want to design a PCA plot by R. Repeatedly I have received this error:

Error in plot.xy(xy, type, ...) : invalid color name 'PopColor'

Popcolor is a column in the popGroups file with this format:

Pop2  Symbol  PopColor  PopColorBg
AFF   0       black     gray
AFF   0       black     gray
ALL   1       red       black
ALL   1       red       black
ALL   1       red       black
AMM   2       green     blue
AMM   2       green     blue
AMM   2       green     blue
AMM   2       green     blue

I would be grateful if someone can help me to solve that problem!

[swbarnes2]

If you want help, you need to do more than this. What command are you using to turn this into a plot?

[hosin]

Hi swbarnes2, Thanks for your respond and your consideration. The R code is:

library(rgl)

fn <- "D:/DD/data/PCA/RUNPCA/plot/eigenvec2.txt"
evecDat <- read.table(fn, skip = 1, col.names = c("Sample", "PC1", "PC2", "Pop"))
indTable = read.table("D:/DD/data/PCA/RUNPCA/plot/MinSS_regions.txt", col.names = c("Sample", "Sex", "Pop2"))

layout(matrix(c(1, 2), ncol = 1), heights = c(1.5, 1))
par(mar = c(4, 4, 0, 0))

merged1EvecDat = merge(evecDat, indTable, by = "Sample")
popGroups = read.table("D:/DD/data/PCA/RUNPCA/plot/popGroups.txt", col.names = c("Pop2", "Symbol", "PopColor", "PopColorBg"))
mergedEvecDat = merge(merged1EvecDat, popGroups, by = "Pop2", all = TRUE)

# Now do some corrections : convert to characters colours (if they are text) and put a default colour for those undefined (in this case "gray")

mergedEvecDat$PopColor <- as.character(mergedEvecDat$PopColor)
mergedEvecDat$PopColorBg <- as.character(mergedEvecDat$PopColorBg)
mergedEvecDat$PopColor[is.na(mergedEvecDat$PopColor)] <- "gray"
mergedEvecDat$Symbol[is.na(mergedEvecDat$Symbol)] <- 9
#mergedEvecDat$PopColor[is.na(mergedEvecDat$PopColor)] <- "gray"

pdf(
  file = "D:/DD/data/PCA/RUNPCA/plot/MyPlot.pdf",
  width = 50,
  height = 25
)

plot(mergedEvecDat$PC2, mergedEvecDat$PC1,
  main = "Name_Of_The_Plot",
  xlim = c(-0.18, 0.16),
  ylim = rev(range(0.11, -0.14)),
  # The plot code continues with symbols used, background, and colour
  pch = mergedEvecDat$Symbol,
  col = mergedEvecDat$PopColor,
  bg = mergedEvecDat$PopColorBg,
  cex = 1, cex.axis = 0.9, cex.lab = 0.9,
  xlab = "PC2", ylab = "PC1")

plot.new()
dev.copy(jpeg,filename="plot.jpg");
par(mar = rep(0, 4))
legend("bottom",
  legend = mergedEvecDat$Pop2,
  pch = mergedEvecDat$Symbol,
  col = mergedEvecDat$PopColor,
  pt.bg = mergedEvecDat$PopColorBg,
  ncol = 14,
  cex = 0.9)
dev.off()