plot_qqR Documentation

QQ plot

Description

Create a Q-Q plot of the test statistics. The x-axis has the theoretical quantile you would expect from a standard normal distribution. The y-axis has the observed quantiles. In the Wald case, it is a ggplot2 version of what you would get from qqnorm and qqline.

Usage

plot_qq(obj, test, test_type = "wt", which_model = "full",
  sig_level = 0.1, point_alpha = 0.2, sig_color = "red",
  highlight = NULL, highlight_color = "green", line_color = "blue")

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.

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 highlighted in the plot. if NULL, no points will be highlighted.

highlight_color

the color to highlight points.

line_color

what color to make the QQ line

Value

a ggplot2 object