Produces a scatter plot from a 'locus' class object using plotly.
scatter_plotly(
loc,
index_snp = loc$index_snp,
pcutoff = 5e-08,
scheme = c("grey", "dodgerblue", "red"),
xlab = NULL,
ylab = NULL,
yzero = (loc$yvar == "logP"),
showLD = TRUE,
LD_scheme = c("grey", "royalblue", "cyan2", "green3", "orange", "red", "purple"),
marker_outline = "black",
marker_size = 7,
recomb_col = "blue",
eqtl_gene = NULL,
beta = NULL,
add_hover = NULL,
showlegend = TRUE,
height = NULL,
webGL = TRUE
)A plotly scatter plot.
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).
x axis title.
y axis title.
Logical whether to force y axis limit to include y=0.
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 r^2 or D' LD results ranging from 0 to 1 in intervals of 0.2. The final colour is for the index SNP.
Specifies colour for outlining points.
Value for size of markers in plotly units.
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.
Column name in loc$data for eQTL genes.
Optional column name for beta coefficient to display upward triangles for positive beta and downward triangles for negative beta (significant SNPs only).
Optional vector of column names in loc$data to add to the
plotly hover text for scatter points.
Logical whether to show a legend for the scatter points.
Height in pixels (optional, defaults to automatic sizing).
Logical whether to use webGL or SVG for scatter plot.
locus() locus_plotly()