Axes and labs for ggplot2

[...]
  labs(x="", y="", fill=paste0(legTitle)) + 
  guides(color=FALSE)+
  scale_y_continuous(breaks = scales::pretty_breaks(n = 10))+
  scale_x_continuous(breaks = scales::pretty_breaks(n = 10)) +
[...]

Theme for ggplot2

theme(
	text = element_text(family=fontFamily),
  panel.grid.major.y =  element_line(colour = "grey", size = 0.5, linetype=1),
  panel.grid.minor.y =  element_line(colour = "grey", size = 0.5, linetype=1),
  panel.background = element_rect(fill = "transparent"),
  panel.grid.major.x =  element_blank(),
  panel.grid.minor.x =  element_blank(),
  axis.title.x = element_text(size=14, hjust=0.5, vjust=0.5),
  axis.title.y = element_text(size=14, hjust=0.5, vjust=0.5),
  axis.text.y = element_text(size=12, hjust=0.5, vjust=0.5),
  axis.text.x = element_text(size=12, hjust=0.5, vjust=0.5),
  plot.title = element_text(hjust=0.5, size = 16, face="bold"),
  plot.subtitle = element_text(hjust=0.5, size = 14, face="italic"),
  legend.title = element_text(face="bold")
)

Transparent background in legend

theme(
	legend.key = element_rect(fill = NA)
)

Save and print file name

For ggplots:

outFile <- file.path(outFolder, paste0("plot_name.", plotType))
ggsave(p, file=outFile, height=myHeight, width=myWidth)
cat(paste0("... written: ", outFile, "\n"))

For base plots:

outFile <- file.path(outFolder, paste0("plot_name.", plotType))
do.call(plotType, list(outFile, height=myHeight, width=myWidth))
[...]
foo <- dev.off()
cat(paste0("... written: ", outFile, "\n"))

Density plot

densplot <- function(x,y, pch=19, cex=1, ...){
	df <- data.frame(x,y)
	d <- densCols(x,y, colramp=colorRampPalette(c("black", "white")))
	df$dens <- col2rgb(d)[1,] + 1L
	cols <- colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
	df$col <- cols[df$dens]
	df <- df[order(df$dens),]
	plot(df$x,df$y, pch=pch, col=df$col, ...)
}

Multiple density curves

plot_multiDens <- function(size_list, plotTit="", legTxt=NULL, legPos="topright", my_ylab="density", my_xlab="") {
  dens <- lapply(size_list, function(x) density(na.omit(x)))
  names(dens) <- names(size_list)
  
  lengthDens <- unlist(lapply(size_list, function(x) length(na.omit(x))))
  
  plot(NA, xlim=range(sapply(dens, "[", "x")), ylim=range(sapply(dens, "[", "y")), 
       main=plotTit, xlab=my_xlab, ylab=my_ylab)
  foo <- mapply(lines, dens, col=1:length(dens))
  if(is.null(legTxt)){
    # legTxt <- names(dens)
    legTxt <- paste0(names(dens), " (n=", lengthDens, ")")
  }
  legend(legPos, legend=legTxt, fill=1:length(dens), bty='n')
}

Print text and write to log file

printAndLog <- function(txt, logFile=""){
  cat(txt)
  cat(txt, file = logFile, append=T)
}

Add correlation to plot

addCorr <- function(x, y, legPos="topright", corMet="pearson", ...) {
  corMet <- tolower(corMet)
  stopifnot(corMet %in% c("pearson", "kendall", "spearman"))
  x_new <- x[!is.na(x) & !is.na(y)]
  y_new <- y[!is.na(x) & !is.na(y)]
  x <- x_new
  y <- y_new
  stopifnot(length(x) == length(y))

  if(length(x) < 3) {
    legTxt <- paste0(paste0(toupper(substr(corMet,1,1)), "CC"), " = NA", "\n", "(# obs. < 3)")
  } else {
    ct <- cor.test(x,y, method = corMet)
    corCoeff <- ct$estimate
    corPval <- ct$p.value
    legTxt <- paste0(paste0(toupper(substr(corMet,1,1)), "CC"), " = ", round(corCoeff, 4), "\n", "(p-val = ", sprintf("%2.2e", corPval), ")")
  }
  legend(legPos, legend = legTxt, ...)
}

Add fitted curve

add_curv_fit <- function(x, y, withR2 = TRUE, R2shiftX = 0, R2shiftY = 0,...) {
  mymodel <- lm(y~x)
  abline(mymodel, ...)
  if(withR2) {
    r2Txt <- paste0("adj. R2 = ", sprintf("%.2f", summary(mymodel)$adj.r.squared))
    r2X <- x[which.min(x)] + R2shiftX
    r2Y <- fitted(mymodel)[which.min(x)]
    text(x = r2X, y = r2Y, 
         labels = r2Txt, 
         adj=c(1,0),
         pos=3,
         cex = 0.7)
  }
}