combining_interaction_and_ChIP_profiles.R

# Initialize the variables
library_path <- "${PATH_T2C}/RLIB"
region <- list("chr" = "chr14", "start" = 54100000, "end" = 54355000)
minimum_signal <- NULL
colour_range <- c(0, 0.0003)
add_borders_to_elements <- FALSE; outfile <- NULL

# Load the libraries and other necessary scripts
infile <- "${sample_name}.reassigned.array.bed"

source(file.path(library_path, "cis_matrix_body.R"))

complete_plot <- p

chipfile <- "CTCF.bedgraph"

source(file.path(library_path, "chip_body.R"))
chip_plot <- p
infile <- "${sample_name}.overlap.bed"

source(file.path(library_path, "cis_matrix_body.R")); subset_plot <- p

require(grid)
require(gtable)

outfile <- "${sample_name}.combined.pdf"
complete_plot2 <- complete_plot + 
  xlab("") + 
  theme(legend.justification=c(0,0), legend.position=c(0.8, 0.4))
chip_plot2 <- chip_plot + 
  coord_fixed(xlim = c(region[["start"]], region[["end"]]), ratio = 200) + 
  xlab("")
subset_plot2 <- subset_plot + 
  scale_y_reverse(labels=NULL) + theme(legend.position="none")
combined_plots <- rbind(
  ggplotGrob(complete_plot2),
  ggplotGrob(chip_plot2),
  ggplotGrob(subset_plot2), size = "last")
pdf(file = outfile, paper = "a4")
grid.newpage()
grid.draw(combined_plots)
dev.off()