gg_scatter {locuszoomr}

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

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.

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.

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).

...

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.

Value

Returns a ggplot2 plot.

See Also

locus() gg_addgenes()

Examples

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)
}