jasper1918

plot_fc<-function(df, key1_x, key1_y, key2_x, key2_y, plot_xlab="", plot_ylab=""){
  l1x<-log2(df[,key1_x] +1)
  l1y<-log2(df[,key1_y] +1)
  l2x<-log2(df[,key2_x] +1)
  l2y<-log2(df[,key2_y] +1)
  diff1 <- l1x - l1y
  diff2 <- l2x - l2y
  
  names(diff1) <- "DIFF1"
  names(diff2) <- "DIFF2"

jasper1918

plot_ma<- function(dat, rep1, rep2, main_title=""){
  l1<-log2(dat[,rep1] +1)
  l2<-log2(dat[,rep2] +1)
  diff <- l1 - l2
  names(diff) <- "LOG2FC"
  ave <- rowMeans(cbind(l1, l2), na.rm=TRUE)
  df <- data.frame(rep1=l1, rep2=l2, "LOG2FC"=diff, "AVE_EXP"=ave, check.names = F)
  max_y<-ceiling(max(abs(max(df$LOG2FC)),abs(min(df$LOG2FC)), 2))
  seq_y<-round(seq(-max_y, max_y, by = .5),1)
  #df$OUT1<-ifelse(abs(df$LOG2FC)>1, 0,1)

jasper1918

# ggplot with equation

lm_eqn <- function(df, key_y, key_x){
  m<-lm(formula(paste(key_y,"~",key_x)), df)
  eq <- substitute(italic(y) == b %.% italic(x) + a*","~~italic(R)^2~"="~r2,
                   list(a = formatC(coef(m)[1], digits = 4,format="f", flag="#"),
                        b = formatC(coef(m)[2], digits = 4,format = "f", flag="#"),
                        r2 = formatC(summary(m)$r.squared, digits = 4,format = "f", flag="#")))
  as.character(as.expression(eq))
}

jasper1918

mypca<-function(x, mytitle="", ...)
{
  par(mfrow=c(1,1))
  this_pc <- prcomp(x, scale=FALSE)
  this_pc_coord <- this_pc$x
  pc1pct=round(summary(this_pc)$importance[2,1]*100,2)
  pc2pct=round(summary(this_pc)$importance[2,2]*100,2)
  par(mar = c(8, 5, 3, 8), xpd=T)
  plot(this_pc_coord[,1], this_pc_coord[,2], pch = 19, cex=2, 

jasper1918

# pairs(df, lower.panel=panel.smooth, upper.panel=panel.cor, diag.panel=panel.hist)

panel.cor <- function(x, y, digits=2, prefix="", cex.cor) 
{
  usr <- par("usr"); on.exit(par(usr)) 
  par(usr = c(0, 1, 0, 1)) 
  r <- abs(cor(x, y)) 
  txt <- format(c(r, 0.123456789), digits=digits)[1] 
  txt <- paste(prefix, txt, sep="") 
  if(missing(cex.cor)) cex <- 0.8/strwidth(txt)