MAplot {MAnorm2}

Generic MA Plotting

Description

MAplot is a generic function used to produce an MA plot. Described here is the default method for plotting on (normalized) signal intensities of two ChIP-seq samples (see also normalize).

Usage

MAplot(x, ...)

## Default S3 method:
MAplot(
  x,
  y,
  occupy.x,
  occupy.y,
  col = NULL,
  pch = NULL,
  ylim = c(-6, 6),
  xlab = "A value",
  ylab = "M value",
  args.legend = list(x = "topright", legend = c("common", "y specific", "x specific",
    "others")),
  ...
)

Arguments

x, y

x is any R object for which a MAplot method has been defined. For the default method, x and y are two numeric vectors representing signal intensities of the 1st and 2nd samples, respectively.

...

Arguments to be passed to specific methods for the S3 generic. For the default method, ... represents further arguments to be passed to plot.

occupy.x, occupy.y

Two logical vectors of occupancy indicators of the two samples.

col, pch

Optional length-4 vectors specifying the colors and point characters of 4 types of genomic intervals: common peak regions, peak regions specific to the 2nd sample, peak regions specific to the 1st sample, and the others. Elements are recycled if necessary.

ylim

A length-two vector specifying the plotting range of Y-axis (i.e., the M value). Each M value falling outside the range will be shrunk to the corresponding limit. Setting the option to NULL to suppress this behavior.

xlab, ylab

Labels for the X and Y axes.

args.legend

A list of arguments to be passed to legend. You may want to modify the default to incorporate actual sample names.

Value

For the default method, MAplot returns NULL.

Note

While it's not strictly required, one typically normalizes the signal intensities (using normalize) prior to calling this function.

Given the typically large number of points to draw, you may want to use alpha to adjust color transparency if you intend to specify col explicitly.

See Also

normalize for performing an MA normalization on ChIP-seq samples; MAplot.bioCond for creating an MA plot on bioCond objects.

Examples

data(H3K27Ac, package = "MAnorm2")
attr(H3K27Ac, "metaInfo")

## Create MA scatter plots on normalized ChIP-seq samples.

# Perform MA normalization directly on all ChIP-seq samples. Exclude the
# genomic intervals in sex chromosomes from common peak regions, since these
# samples are from different genders.
autosome <- !(H3K27Ac$chrom %in% c("chrX", "chrY"))
norm <- normalize(H3K27Ac, 4:8, 9:13, common.peak.regions = autosome)

# MA plot on two samples from the same individual.
legend <- c("common", "GM12891_2 specific", "GM12891_1 specific", "others")
MAplot(norm[[5]], norm[[6]], norm[[10]], norm[[11]],
       args.legend = list(x = "topright", legend = legend),
       main = "GM12891_rep1 vs. GM12891_rep2")
abline(h = 0, lwd = 2, lty = 5)

# MA plot on two samples from different individuals.
legend <- c("common", "GM12891_1 specific", "GM12890_1 specific", "others")
MAplot(norm[[4]], norm[[5]], norm[[9]], norm[[10]],
       args.legend = list(x = "topright", legend = legend),
       main = "GM12890_rep1 vs. GM12891_rep1")
abline(h = 0, lwd = 2, lty = 5)