GenoView (version 1.6.0)

plotExonRect: Plot Rectangular Exon Components

Description

Adds colored rectangular blocks, denoting exon components such as coding sequences or untranslated regions, to a ggplot. Provides filtering to highlight a subset of the input data in the plot.

Usage

plotExonRect(plt, component = c("cds", "utr"), comp.df,
col.name = "type", filt.by.comp = FALSE, size = c(0.4, 0.15), 
subset.df, comp.col = "dark grey", 
sub.col = RColorBrewer::brewer.pal(3, "Set1")[2], 
aesCst)

Arguments

plt

A ggplot object

component

Exon component string, such as "cds", "utr"

comp.df

Exon components data.frame, contains a col.name column which contains exon component strings and columns for start, end, and stepping (starting y position in plot)

col.name

Column name used to filter comp.df before plotting

filt.by.comp

Determines if comp.df should be filtered for component contents before plotting

size

Half the height of the rectangular blocks

subset.df

Secondary data.frame, contains a col.name column which contains exon component strings and columns for start, end, and stepping (starting y position in plot). This data is plotted in a highlighting colour.

comp.col

Colour of data in code.df

sub.col

Highlighting colour of data in subset.df

aesCst

Custom aes function which can handle constants in variables

Value

ggplot object with additional geom_rect() layers

Examples

library(ggplot2)

set.seed(3)
N = 30
# Create sample base exon components
starts = sample(1:10000, size = N, replace = TRUE)
sample.df <- data.frame(start = starts, 
                        end = starts + sample(100:500, size = N), 
                        stepping = 1, 
                        type = sample(c("cds", "utr", "gap"), 
                                        size = N, replace = TRUE))

# Create sample highlighted exon components
N = 5
starts = sample(1:10000, size = N, replace = TRUE)
sample.sub <- data.frame(start = starts, 
                        end = starts + sample(100:500, size = N), 
                        stepping = 1, 
                        type = sample(c("cds", "utr", "gap"), 
                                        size = N, replace = TRUE))

# Using an aes function which evaluates arguments locally without parsing
aesCst <- function(...) {
    structure(list(...),  class = "uneval")
}

step1 <-ggplot() + 
        geom_abline(intercept = 1, slope = 0, 
                    aes(xmin = -1, xmax = 1, ymin = 0.5, ymax = 1.5), 
                    color = "dark grey")
                    
step2 <- plotExonRect(plt = step1, component = "cds", comp.df = sample.df, 
                        filt.by.comp = TRUE, size = 0.4, subset.df = sample.sub, 
                        aesCst = aesCst)
plotExonRect(plt = step2, component = "utr", comp.df = sample.df, 
                        filt.by.comp = TRUE, size = 0.15, subset.df = sample.sub, 
                        aesCst = aesCst)