time course plotting function

plot-timecourse.r

timecourse <- readRDS('timecourse.rds')

plot.timecourse <- function(gene.list, east.color='orange', west.color='forestgreen', double.plot=FALSE, side.by.side=FALSE) {
  library(ggplot2)
  timecourse.subset <- timecourse[timecourse$gene %in% gene.list, ]
  timecourse.subset$gene <- as.character(timecourse.subset$gene)

  if (double.plot) {
    timecourse.subset.copy <- timecourse.subset
    timecourse.subset.copy$hour <- timecourse.subset.copy$hour + 48
    timecourse.subset <- rbind(timecourse.subset, timecourse.subset.copy)
    x.breaks <- seq(0, 96, 12)
  } else {
    x.breaks <- seq(0, 48, 12)
  }

  p <- ggplot(timecourse.subset, aes(x=hour, y=mean, color=side)) +
         geom_line(size=1) +
         geom_errorbar(aes(ymin=mean-stderr, ymax=mean+stderr), alpha=0.35) +
         labs(x = 'Time (hours)', y = 'Mean Normalized Counts') +
         scale_x_continuous(breaks=x.breaks) +
         scale_color_manual(name = 'Orientation',values = c(east.color, west.color))

  if (side.by.side) {
    p <- p + facet_grid(gene ~ side, scales='free_y')
  } else {
    p <- p + facet_wrap(~ gene, ncol=1, scales='free_y')
  }

  print(p)
}

# Plot single gene
plot.timecourse('Ha412v1r1_07g008930')

# Plot gene list
gene.list <- c('Ha412v1r1_07g008930', 'Ha412v1r1_01g020690', 'Ha412v1r1_16g004440', 'Ha412v1r1_14g049950')
plot.timecourse(gene.list)

# Double plot
plot.timecourse(gene.list, d=T)

# Plot East/West side-by-side
plot.timecourse(gene.list, s=T)

# Save most recent plot (set width/height using w/h)
ggsave('timecourse-demo-plot.png', w=4, h=6)