plot_pairwise_ld_heatmap: Create a heatmap from pairwise linkage data.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Create a heatmap from pairwise linkage data.

Description

Prepares a ggplot2 heatmap from pairwise linkage disequilibrium data stored in a snpRdata object.

Usage

plot_pairwise_ld_heatmap(
  x,
  facets = NULL,
  snp.subfacet = NULL,
  sample.subfacet = NULL,
  LD_measure = "CLD",
  r = NULL,
  l.text = "CLD",
  viridis.option = "inferno",
  gradient_colors = NULL,
  title = NULL,
  t.sizes = c(16, 13, 10, 12, 10),
  background = "white",
  simplify_output = FALSE
)

Arguments

x	snpRdata object.
facets	character, default NULL. Categorical metadata variables by which to break up plots. Must match facets for which LD data has been previously calculated, and only a single facet can be plotted at once. See Facets_in_snpR for more details.
snp.subfacet	character, default NULL. Specific snp-specific levels of the provided facet to plot. See examples.
sample.subfacet	character, default NULL. Specific sample-specific levels of the provided facet to plot. See examples.
LD_measure	character, default rsq. LD metric to plot. Must be present in the calculated LD data.
r	Numeric. Region of the chromosome to subset and plot. Given in kb in the format numeric vector c(lower, upper).
l.text	character, default "CLD". Legend title.
viridis.option	character, default "inferno". Viridis color scale option to use. Other color scales may be substituted by appending the scale_color_continuous and scale_fill_continuous ggplot functions to the produced plot using the '+' operator. See scale_gradient for details.
gradient_colors	character vector of length 2 or NULL, default NULL. If provided, the low and high LD colors for the color scale. Provided as an alternative to the viridis scales. Take care to set a background color not on this scale. For example, c("white", "black") is an excellent choice, but will make missing data inaccurately appear appear as if it has a very low LD unless a different background color is selected.
title	character. Plot title.
t.sizes	numeric, default c(16, 13, 10, 12, 10). Text sizes, given as c(title, legend.title, legend.ticks, axis, axis.ticks).
background	character, default "white". Background color for plot.
simplify_output	If TRUE, only the ggplot object will be return. This is optimal, since the data is already returned in that object, but is not the default due to backwards consistency with old code.

Details

Since the output is a ggplot object, options can be added or changed by adding "+ function()" to the end of LD_pairwise_heatmap. Some common options are also built into this function as arguments, but can be overwritten freely.

Specific facets and facet levels can be requested as long as LD data for those facets has been previously calculated. Facets should be provided as described in Facets_in_snpR. Only one facet can be plotted at once. Plots for individual SNP or sample-specific facet levels for the specified facet can also be requested. See examples. For facets with many categories, this is strongly recommended, since plots with many facet levels become computationally challenging to produce and difficult to interpret. A facets argument of NULL will plot the base level facet, a facet argument of "all" is not accepted.

Note that NA LD values will be colored white in the resulting plot.

Value

A list containing:

• plot: A pairwise LD heatmap as a ggplot object.

• dat: Data used to generate the ggplot object.

If simplify_output is FALSE, only the ggplot object is returned.

Author(s)

William Hemstrom

Nicholas Sard

Examples

## Not run: 
# get LD data
dat <- calc_pairwise_ld(stickSNPs, c("pop.chr"))

# produce plots for linkage group IX in the ASP and CLF populations.
plot_pairwise_ld_heatmap(dat, c("pop.chr"), "groupIX", c("ASP", "CLF"))

# produce plots for every population for linkage group IV
plot_pairwise_ld_heatmap(dat, c("pop.chr"), "groupIV")

## End(Not run)

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.