plot_volcanoR 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