R: Plot volcano plot

plot_volcano

R Documentation

Plot volcano plot

Description

Plot a volcano plot. A volcano plot is a plot of beta value (regression coefficient) vs. log(significance). Ideally, it looks like a volcano; more significance typically results in higher beta

Usage

plot_volcano(obj, test, test_type = "wt", which_model = "full",
  sig_level = 0.1, point_alpha = 0.2, sig_color = "red",
  highlight = NULL)

Arguments

`obj`	a `sleuth` object
`test`	a character string denoting which beta to use for highlighting the transcript
`test_type`	either 'wt' for wald test or 'lrt' for likelihood ratio test. NB: Currently only the wald test is supported.
`which_model`	a character string denoting which model to use for the test
`sig_level`	the significance level for Fdr
`point_alpha`	the alpha for the points
`sig_color`	what color to make the 'significant' transcripts
`highlight`	a `data.frame` with one column, `target_id`. These points will be displayed below in a table.

Value

a ggplot object