Produces a base graphics scatter plot from a 'locus' class object. This
function is called by locus_plot() to generate the scatter plot portion.
Can be used manually with set_layers().
scatter_plot(
loc,
index_snp = loc$index_snp,
pcutoff = 5e-08,
scheme = c("grey", "dodgerblue", "red"),
cex = 1,
cex.axis = 0.9,
cex.lab = 1,
xlab = NULL,
ylab = NULL,
ylim = NULL,
ylim2 = c(0, 100),
yzero = (loc$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,
label_x = 4,
label_y = 4,
eqtl_gene = NULL,
beta = NULL,
add = FALSE,
align = TRUE,
...
)No return value. Produces a scatter plot using base graphics.
Object of class 'locus' to use for plot. See locus.
Specifies index SNP or a vector of SNPs 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.
Cut-off for p value significance. Defaults to p = 5e-08. Set
to NULL to disable.
Vector of 3 colours if LD is not shown: 1st = normal points, 2nd = colour for significant points, 3rd = index SNP(s).
Specifies size for points.
Specifies font size for axis numbering.
Specifies font size for axis titles.
x axis title.
y axis title.
y axis limits (y1, y2).
Secondary y axis limits for recombination line, if present.
Logical whether to force y axis limit to include y=0.
Logical whether x axis numbers and axis title are plotted.
Logical whether a bounding box is plotted around upper and lower plots.
Logical whether to show LD with colours
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.
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.
Offset from 0-1 which shifts the scatter plot up and recombination line plot down. Recommended value 0.1.
Position of legend. See legend(). Set to NULL to hide
legend.
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.
Value or vector for position of label as percentage of x axis scale.
Value or vector for position of label as percentage of y axis scale.
Column name in loc$data for colouring eQTL genes.
Optional column name for beta coefficient to display upward triangles for positive beta and downward triangles for negative beta (significant SNPs only).
Logical whether to add points to an existing plot or generate a new plot.
Logical whether to set par() to align the plot.
Other arguments passed to plot() to control the scatter plot
e.g. main, ylim etc.
Advanced users familiar with base graphics can customise every single point
on the scatter plot, by adding columns named bg, col, pch or cex
directly to the dataframe stored in $data element of the 'locus' object.
Setting these will overrule any default settings. These columns refer to
their respective base graphics arguments, see graphics::points().
locus() set_layers()