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bedgraph-visualizer.R #4

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31 changes: 21 additions & 10 deletions bedgraph-visualizer.R
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,10 @@ genome_plot <- function() {
lrr_plot <- ggplot(lrr_chr_data) +
geom_point(aes(x = Start, y = LRR), color = "#2a2a2a") +
geom_line(data = smooth_line, aes(x = Pos, y = LRR), color = "#ff3333") + # Use the custom smooth line
geom_rect(aes(xmin = min(Start), xmax = min(Start) + 100000, ymin = -Inf, ymax = Inf),
fill = "yellow", alpha = 0.005) + # Highlight start of CNV region with transparent orange
geom_rect(aes(xmin = max(Start) - 100000, xmax = max(Start), ymin = -Inf, ymax = Inf),
fill = "yellow", alpha = 0.005) + # Highlight end of CNV region with transparent orange
theme_minimal() +
labs(x = NULL, y = "LRR", title = paste("chr", chr, sep="")) +
geom_hline(yintercept = 0, linetype = "dotted", color = "#555555") + # Guide line for LRR at y = 0
Expand Down Expand Up @@ -117,7 +121,6 @@ genome_plot <- function() {
ggsave(output_file, plot = combined_plot, width = 30, height = 40, dpi = 300)
}

# Function to plot specific regions
region_plot <- function(region_file, min_padding=600000) {
# Load region data
regions <- read.table(region_file, header = FALSE)
Expand All @@ -126,39 +129,47 @@ region_plot <- function(region_file, min_padding=600000) {
# Iterate over each region and create plots
for (i in 1:nrow(regions)) {
region <- regions[i, ]
padding = (region$End - region$Start )
padding = (region$End - region$Start)
if (padding <= min_padding) {
padding = min_padding
}
padded_start = region$Start - padding
padded_end = region$End + padding

# Filter BAF and LRR data for the current region
filtered_baf <- baf_data %>%
filtered_baf <- baf_data %>%
filter(Chr == region$Chr & Start >= padded_start & Start <= padded_end)

filtered_lrr <- lrr_data %>%
filtered_lrr <- lrr_data %>%
filter(Chr == region$Chr & Start >= padded_start & Start <= padded_end)

smooth_line <- getSmoothLine(filtered_lrr, region)

# Create the LRR plot with smooth line

lrr_plot <- ggplot(filtered_lrr) +
geom_point(aes(x = Start, y = LRR), color = "#2a2a2a") +
geom_line(data = smooth_line, aes(x = Pos, y = LRR), color = "#ff3333") + # Use the custom smooth line
geom_point(aes(x = Start, y = LRR), color = "#2a2a2a", size= 0.3) +
geom_line(data = smooth_line, aes(x = Pos, y = LRR), color = "#ff3333") + # Use the custom smooth line
theme_minimal() +
labs(x = NULL, y = "LRR", title = paste(region$Chr, ":", region$Start, "-", region$End, sep="")) +
geom_hline(yintercept = 0, linetype = "dotted", color = "#555555") + # Guide line for LRR at y = 0
coord_cartesian(ylim = c(-1, 1)) + # Set the y-axis limits for LRR
scale_x_continuous(labels = label_number()) # Format x-axis labels as numeric
scale_x_continuous(labels = label_number()) + # Format x-axis labels as numeric
# Highlight the CNV region with more transparent orange
geom_rect(aes(xmin = region$Start, xmax = region$End, ymin = -Inf, ymax = Inf),
fill = "yellow", alpha = 0.005, inherit.aes = FALSE) # More transparent orange rectangle

# Create the BAF plot
# Create the BAF plot with highlight at CNV region
baf_plot <- ggplot(filtered_baf) +
geom_point(aes(x = Start, y = BAF), color = "#2a2a2a") +
geom_point(aes(x = Start, y = BAF), color = "#2a2a2a", size= 0.3) +
theme_minimal() +
labs(x = "Position", y = "BAF") +
geom_hline(yintercept = 0.5, linetype = "dotted", color = "#555555") + # Guide line for BAF at y = 0.5
coord_cartesian(ylim = c(0, 1)) +
scale_x_continuous(labels = label_number()) # Format x-axis labels as numeric
scale_x_continuous(labels = label_number()) + # Format x-axis labels as numeric
# Highlight the CNV region with more transparent orange
geom_rect(aes(xmin = region$Start, xmax = region$End, ymin = -Inf, ymax = Inf),
fill = "yellow", alpha = 0.005, inherit.aes = FALSE) # More transparent orange rectangle

# Combine the plots vertically
combined_plot <- plot_grid(lrr_plot, baf_plot, align = "v", ncol = 1, rel_heights = c(1, 1))
Expand Down