plot.R

library(ncgchts)
library(ggplot2)
library(RColorBrewer)
library(stringr)
data(sample.info)
con <- get.connection('hts', 'ncgc', 'probedb')
curve.order <- c(-1.1, -1.2, -2.1, -2.2, -1.3, -2.3, -1.4, -2.4,  1.1, 1.2, 2.1, 2.2, 1.3, 2.3, 1.4, 2.4, -3.0, 3.0, 4.0, 5.0)

protos <- c('s-levens-topo-HCT116-1', 's-levens-topo-mutant-1')
curves <- lapply(protos, function(p) {
  proto <- query.protocol(con, p, 'activity')
  proto <- data.frame(proto, prefix=I(base.id(proto$SID)), sdt=I("activity"), protocol=I(p))
  proto <- dedup.curves(proto)
  return(proto)
})
curves <- do.call(rbind,curves)

sids <- read.table(textConnection('NCGC00250412-01
NCGC00344588-01'), header=FALSE, as.is=TRUE)

cols <- brewer.pal(2, 'Set1')
junk <- apply(sids, 1,  function(row) {
  sid <- row[1]

  dat <- subset(curves, base.id(SID) == base.id(sid))
  dat <- dat[order(dat$protocol),]
  if (nrow(dat) == 0) {
    cat("No data for",sid, '\n')
    return(NA)
  }
  
  dat <- data.frame(dat, pch=c(15,16), col=c('black', 'red'))
  print(dat[, c('protocol', 'col')])
  names(dat)[1] <- 'sdid'
  par(mar=c(4.2, 4.2, 1,1), cex=1.2, cex.axis=0.8, cex.lab=1.1, tcl=-0.5 * 1)
  if (is.na(dat$sdid[1])) {
    cat("***", sid, '\n')
    return(NA)
  } else {
    junk <- plot.hill2(con, dat, force=TRUE, lwd=2,
                       xlab='log Concentration (M)', ylab='% Response', ylim=c(0, 130),
                       las = 1
                       )
    sname <- subset(sample.info, base.id(SAMPLE_ID) == base.id(sid))$SAMPLE_NAME[1]
    dev.copy(pdf, sprintf("topo-%s-%s.pdf", sid, sname), 6, 6/1.618);dev.off()
    ##return(with(dat, TAUC[1] - TAUC[2]))
  }
})