MAplot.bioCond: Create an MA Plot on Two 'bioCond' Objects

In MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples

Create an MA Plot on Two bioCond Objects

Description

Given two bioCond objects, the function draws an MA plot, which is a scatter plot with signal intensity differences between the two conditions against the average signal intensities across conditions.

Usage

## S3 method for class 'bioCond'
MAplot(
  x,
  y,
  col = NULL,
  pch = NULL,
  ylim = c(-6, 6),
  xlab = "A value",
  ylab = "M value",
  plot.legend = TRUE,
  ...
)

Arguments

x, y	Two bioCond objects.
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 condition, peak regions specific to the 1st condition, 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.
plot.legend	A logical value indicating whether to add a legend.
...	Further arguments to be passed to plot.

Details

Genomic intervals are classified based on the occupancy field in each of the two bioCond objects. See bioCond for a full description of the structure of a bioCond object.

Value

The function returns NULL.

Note

While it's not strictly required, ChIP-seq samples contained in the two bioCond objects are expected to have been normalized prior to calling this function. These samples could be normalized all together before being classified into biological conditions (via normalize). Alternatively, normalization can also be performed at the level of bioCond objects (via normBioCond).

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

bioCond for creating a bioCond object; MAplot.default for producing an MA plot on normalized signal intensities of two ChIP-seq samples; normalize for performing an MA normalization on ChIP-seq samples; normBioCond for normalizing a set of bioCond objects.

Examples

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

## Create MA scatter plots for the comparisons between individuals.

# Perform the MA normalization and construct bioConds to represent
# individuals.
norm <- normalize(H3K27Ac, 4, 9)
norm <- normalize(norm, 5:6, 10:11)
norm <- normalize(norm, 7:8, 12:13)
conds <- list(GM12890 = bioCond(norm[4], norm[9], name = "GM12890"),
              GM12891 = bioCond(norm[5:6], norm[10:11], name = "GM12891"),
              GM12892 = bioCond(norm[7:8], norm[12:13], name = "GM12892"))
autosome <- !(H3K27Ac$chrom %in% c("chrX", "chrY"))
conds <- normBioCond(conds, common.peak.regions = autosome)

# MA plots on pairs of individuals.
MAplot(conds[[1]], conds[[2]], main = "GM12890 vs. GM12891")
abline(h = 0, lwd = 2, lty = 5)
MAplot(conds[[1]], conds[[3]], main = "GM12890 vs. GM12892")
abline(h = 0, lwd = 2, lty = 5)
MAplot(conds[[2]], conds[[3]], main = "GM12891 vs. GM12892")
abline(h = 0, lwd = 2, lty = 5)

MAnorm2 documentation built on Oct. 29, 2022, 1:12 a.m.