gg_scatter: Locus scatter plot using ggplot2

Description

Produces a scatter plot from a 'locus' class object (without gene tracks).

Usage

gg_scatter(
  loc,
  index_snp = loc$index_snp,
  pcutoff = 5e-08,
  scheme = c("grey", "dodgerblue", "red"),
  size = 2,
  cex.axis = 1,
  cex.lab = 1,
  xlab = NULL,
  ylab = NULL,
  ylim = NULL,
  ylim2 = c(0, 100),
  yzero = (loc$yvar == "logP"),
  xticks = TRUE,
  border = FALSE,
  showLD = TRUE,
  LD_scheme = c("grey", "royalblue", "cyan2", "green3", "orange", "red", "purple"),
  recomb_col = "blue",
  recomb_offset = 0,
  legend_pos = "topleft",
  labels = NULL,
  eqtl_gene = NULL,
  beta = NULL,
  shape = NULL,
  shape_values = c(21, 24, 25),
  ...
)

Value

Returns a ggplot2 plot.

Arguments

loc: Object of class 'locus' to use for plot. See locus.
index_snp: Specifies index SNP to be shown in a different colour and symbol. Defaults to the SNP with the lowest p-value. Set to NULL to not show this.
pcutoff: Cut-off for p value significance. Defaults to p = 5e-08. Set to NULL to disable.
scheme: Vector of 3 colours if LD is not shown: 1st = normal points, 2nd = colour for significant points, 3rd = index SNP.
size: Specifies size for points.
cex.axis: Specifies font size for axis numbering.
cex.lab: Specifies font size for axis titles.
xlab: x axis title.
ylab: y axis title.
ylim: y axis limits (y1, y2).
ylim2: Secondary y axis limits for recombination line.
yzero: Logical whether to force y axis limit to include y=0.
xticks: Logical whether x axis numbers and axis title are plotted.
border: Logical whether a bounding box is plotted around the plot.
showLD: Logical whether to show LD with colours
LD_scheme: Vector of colours for plotting LD. The first colour is for SNPs which lack LD information. The next 5 colours are for r2 or D' LD results ranging from 0 to 1 in intervals of 0.2. The final colour is for the index SNP.
recomb_col: Colour for recombination rate line if recombination rate data is present. Set to NA to hide the line. See link_recomb() to add recombination rate data.
recomb_offset: Offset from 0-1 which shifts the scatter plot up and recombination line plot down. Recommended value 0.1.
legend_pos: Position of legend. Set to NULL to hide legend.
labels: Character vector of SNP or genomic feature IDs to label. The value "index" selects the highest point or index SNP as defined when locus() is called. Set to NULL to remove all labels.
eqtl_gene: Optional column name in loc$data for colouring eQTL genes.
beta: Optional column name for beta coefficient to display upward triangles for positive beta and downward triangles for negative beta (significant SNPs only).
shape: Optional column name in loc$data for controlling shapes. beta and shape cannot both be set. This column is expected to be a factor.
shape_values: Vector of shape values which match levels of the column specified by shape. This vector is passed to ggplot2::scale_shape_manual() as the argument values. See points() for a list of shapes and the numbers they map to.
...: Optional arguments passed to geom_text_repel() to configure label drawing.

Details

If recombination rate data is included in the locus object following a call to link_recomb(), this is plotted as an additional line with a secondary y axis. In the base graphics version the line is placed under the scatter points, but this is not possible with ggplot2 as the secondary y axis data must be plotted on top of the primary scatter point data.

Examples

Run this code

if(require(EnsDb.Hsapiens.v75)) {
data(SLE_gwas_sub)
loc <- locus(SLE_gwas_sub, gene = 'IRF5', flank = c(7e4, 2e5), LD = "r2",
             ens_db = "EnsDb.Hsapiens.v75")
gg_scatter(loc)
}