easyManhattan: Interactive Manhattan plot labels

In easylabel: Interactive Scatter Plot and Volcano Plot Labels

Interactive Manhattan plot labels

Description

Interactive labelling of Manhattan plots using 'shiny' and 'plotly' interface.

Usage

easyManhattan(
  data,
  chrom = "chrom",
  pos = "pos",
  p = "p",
  labs = "rsid",
  startLabels = NULL,
  pcutoff = 5e-08,
  chromGap = NULL,
  chromCols = c("royalblue", "skyblue"),
  sigCol = "red",
  alpha = 0.7,
  labelDir = "horiz",
  xlab = "Chromosome position",
  ylab = expression("-log"[10] ~ "P"),
  xlim = NULL,
  ylim = NULL,
  outline_col = NA,
  shapeScheme = 16,
  size = 6,
  width = ifelse(transpose, 600, 1000),
  height = ifelse(transpose, 800, 600),
  lineLength = 60,
  npoints = max(c(nrow(data)/5, 1e+06)),
  nplotly = 1e+05,
  npeaks = NULL,
  span = 2e+07,
  transpose = FALSE,
  filename = NULL,
  ...
)

Arguments

data	The dataset (data.frame or data.table) for the plot.
chrom	The column of chomosome values in data.
pos	The column of SNP positions in data.
p	The column of p values in data.
labs	The column of labels in data.
startLabels	Vector of initial labels. With a character vector, labels are identified in the column specified by labs. With a numeric vector, points to be labelled are referred to by row number.
pcutoff	Cut-off for p value significance. Defaults to 5E-08.
chromGap	Size of gap between chromosomes along the x axis in base pairs. If NULL this is automatically calculated dependent on the size of the genome. Default is around 3E07 for a human genome, and smaller for smaller genomes.
chromCols	A vector of colours for points by chromosome. Colours are recycled dependent on the length of the vector.
sigCol	Colour for statistically significant points. Ignored if set to NA.
alpha	Transparency for points.
labelDir	Option for label lines. See easylabel().
xlab	x axis title. Accepts expressions.
ylab	y axis title. Accepts expressions.
xlim	The x limits (x1, x2) of the plot.
ylim	The y limits of the plot.
outline_col	Colour of symbol outlines. Passed to easylabel().
shapeScheme	A single symbol for points or a vector of symbols. Passed to easylabel().
size	Specifies point size. Passed to easylabel().
width	Width of the plot in pixels. Saving to pdf scales 100 pixels to 1 inch.
height	Height of the plot in pixels.
lineLength	Initial length of label lines in pixels.
npoints	Maximum number of points to plot when saving the final plot to pdf. By default plots with >1 million points are thinned to speed up plotting. Setting a value of NA will plot all points.
nplotly	Maximum number of points to display via plotly. We recommend the default setting of 100,000 points (or fewer).
npeaks	Number of peaks to label initially.
span	a peak is defined as the most significant SNP within a window of width span centred at that SNP.
transpose	Logical whether to transpose the plot.
filename	Filename for saving to pdf.
...	Other arguments passed to easylabel().

Value

By default no return value. If output_shiny = FALSE or the shiny button 'Export plotly & exit' is pressed, a plotly figure is returned. See easylabel().

See Also

easylabel() easyVolcano()

easylabel documentation built on May 29, 2024, noon