Visualisation

library(CAMDAC)

CAMDAC produces several output files that visualise the copy number state. DNA methylation rates can be passed to external packages for visualisation. For a quick view of DMRs in R:

library(data.table)
library(ggplot2)

# Show DMPs around a region
dmr <- data.table(dmr) # Object from CAMDAC output *annotated_DMRs.fst
dmp <- data.table(dmp) # Object from CAMDAC *results_per_CpG.fst
chrome <- dmr[1, ]$chrom
starte <- dmr[1, ]$start
ende <- dmr[1, ]$end
offset <- 1000 # Offset 1kB either side of region
dmp <- data.table(dmp)
dm_regions <- dmp[chrom == as.character(chrome) & start >= (starte - offset) & end <= (ende + offset), ]

# Using ggplot, generate a geom where the m_t values are
tplt <- ggplot(dm_regions, aes(x = start)) +
  geom_point(aes(y = m_t), color = "skyblue") +
  geom_point(aes(y = m_n), color = "grey") +
  geom_vline(aes(xintercept = start, color = DMP_t)) +
  theme_classic() +
  scale_color_manual(values = c("skyblue", "blue")) +
  scale_y_continuous(limits = c(0, 1)) +
  geom_vline(xintercept = c(start, end), color = "red", linetype = "dashed") +
  labs(x = dm_regions$chrom[[1]])
tplt

CAMDAC DMR Visualization

Here, light blue dots are the pure tumour, while light-grey are the normal. The red dash is the DMR region and the vertical lines are hypomethylated DMPs (blue) and hypermethylated DMPs (light blue).