plotPairwise: Plot Pairwise Values from a GRangeList

In steveped/chipExtra: Additional functions for working with ChIP-Seq data

Plot Pairwise Values from a GRangeList

Description

Plot Pairwise Values from a GRangeList by overlapping GRanges

Usage

plotPairwise(
  x,
  var,
  colour,
  label,
  index = c(1, 2),
  p = 0,
  method = "union",
  ignore.strand = TRUE,
  min_width = 0,
  xside = c("boxplot", "density", "violin", "none"),
  yside = c("boxplot", "density", "violin", "none"),
  side_panel_width = c(0.3, 0.4),
  side_alpha = 1,
  xside_axis_pos = "right",
  yside_axis_label = scales::label_wrap(10),
  smooth = TRUE,
  rho_geom = c("text", "label", "none"),
  rho_col = "black",
  rho_size = 4,
  rho_pos = c(0.05, 0.95),
  rho_alpha = 1,
  label_geom = c("label_repel", "label", "text_repel", "text", "none"),
  label_width = 20,
  label_sep = "; ",
  label_size = 3.5,
  label_alpha = 0.7,
  min_d = 1,
  group_sep = " - ",
  simplify_equal = TRUE,
  name_sep = " ",
  plot_theme = theme_get(),
  ...
)

Arguments

x	A GRangesList
var	The colunm to compare between list elements
colour	Optional column to use for combining across elements and setting point colour
label	Optional column to use for labelling ranges with the most extreme changes
index	Which list elements to compare
p, method, ignore.strand, min_width	Passed to makeConsensus()
xside, yside	Will call geom_(x/y)side* from the package ggside and show additional panels on the top and right of the plot respectively
side_panel_width	Set the relative widths of the side panels
side_alpha	Set fill transparency in side panels
xside_axis_pos	Position for axis_labels in the top panel when using a discrete axis
yside_axis_label	Wrapping for axis labels on the right-side panel when using a discrete axis. Set to waiver() to turn off wrapping
smooth	logical(1). If TRUE a regression line will be drawn using geom_smooth. To add this manually, set to FALSE and call this geom with any custom parameters after creating the plot
rho_geom	Used to add correlation coefficients for the two values
rho_col, rho_size, rho_alpha	Parameters for displaying the correlation
rho_pos	Place the correlation coefficient within the plotting region
label_geom	Used to add labels from the column specified in label
label_width	Label text will be truncated to this length
label_sep	If multiple values (e.g. genes) are mapped to a range, separate values using this string
label_size, label_alpha	Passed to the geom used for adding labels
min_d	Labels will only be added if the points lie circle beyond a sircle of this radius
group_sep	Text separator used to separate categories when specifying colour
simplify_equal	logical(1) When combining columns from both elements for the colour categories, should shared values be annotated as 'Both ...' instead of having longer, more difficult to read annotations.
name_sep	Character string to separate names of the GRangesList and the selected column. Will appear as axis-labels
plot_theme	Sets the initial theme by using the default theme for the current R session via get_theme()
...	Passed to geom_point() for the main panel

Details

This function enables pairwise plotting of two elements within a GRangesList. All elements of the GRangesList will contain the same columns, so a set of consensus ranges are first formed, before then taking all values from each GRangesList element which overlap the range and producing a piarwise plot.

Given that not all ranges will have values in both elements, side panels are produced which can show the distribution of plotted values, along with those which are only found in one of the foundational GRanges. These can take the form of density, violin or boxplots.

Addition columns, such as Differential Signal status can also be used to form pairwise groups and colour the points.

If a column in the GRangesList is suitable for labelling points, such as a column with genes mapped to each range, this can be specified using the argument label = "col_to_label". Only the furthest point from the origin will be labelled within each group used to colour the points. Labels will only be added if they lie beyond a circle of radius min_d from the origin. If multiple genes are mapped to the range, these will be separated by the string provided in the label_sep argument.

A regression line and correlation co-efficient are added to the plot by default, but can be hidden easily if preferred

Value

A ggside or ggplot2 object

Examples

theme_set(theme_bw())
set.seed(100)
gr1 <- GRanges(paste0("chr1:", seq(10, 150, by = 10)))
width(gr1) <- 5
gr1$logFC <- rnorm(length(gr1))
gr1$FDR <- rbeta(length(gr1), 1, 8)

gr2 <-  GRanges(paste0("chr1:", seq(51, 250, by = 15)))
width(gr2) <- 4
gr2$logFC <- rnorm(length(gr2))
gr2$FDR <- rbeta(length(gr2), 1, 8)
grl <- GRangesList(TF1 = gr1, TF2 = gr2)
grl <- addDiffStatus(grl)

# Using the defaults
plotPairwise(grl, var = "logFC")

# Density plots on the side panels
plotPairwise(
  grl, var = "logFC", xside = "density", yside = "density",
  side_alpha = 0.5
)

# Turning off side panels, regression line and correlations
plotPairwise(
  grl, var = "logFC", xside = "none", yside = "none",
  rho_geom = "none", smooth = FALSE
)

# Add colours using the status column
plotPairwise(grl, var = "logFC", colour = "status") +
  scale_fill_manual(values = rep_len(c("blue", "red", "white", "grey"), 8)) +
  guides(fill = "none")

steveped/chipExtra documentation built on Aug. 1, 2024, 12:33 a.m.