manhattan: manhattan

In chiragjp/xwas: X-Wide Association Analyses

Description

Takes output of the xwas function to display as a manhattan plot.

Usage

manhattan(data, qthreshold = 0.05, nlabels = 0, ylab = expression(-log[10]
  * "(p-value)"), frame.plot = FALSE, pch = 20, legend = FALSE,
  group.by = NULL, group.label = NULL, group.col = NULL, ...)

Arguments

data	is the vector containing a list of p-values to display in a manhattan plot.
qthreshold	is the cutoff of significance (the q-value).
nlabels	is the number of top hits to label.
ylab	is a default y-axis label passed on to the plot function.
frame.plot	is the option passed on to the plot function.
pch	is default to 20 setting the point type to a small bullet in the plot function.
legend	is default to FALSE but will put a legend in the upper right corner if TRUE.
group.by	is a data.frame object with n rows and 2 columns. Ideally one of the columns is named "var" but some logic is built in to try and decipher the appropriate column by percentage of matches.
group.label	is a character vector of labels for each of the groups.
group.col	is a color palette of for each group. It's an optional argument and defaults to the rainbow palette. If provided, it should be the same length at group.label as it is a 1:1 match.
...	are additional arguments passed onto the plot function.

Value

none

Examples

## Not run: 
manhattan()
manhattan(glucose, main="XWAS of LBXGLU")

## End(Not run)

chiragjp/xwas documentation built on May 13, 2019, 5:27 p.m.