plot_essentiality: Plot the essentiality of a library as per DeJesus et al.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Plot the essentiality of a library as per DeJesus et al.

Description

This provides a plot of the essentiality metrics 'zbar' with respect to gene. In my pipeline, I use their stand alone mh_ess and tn_hmm packages. The result files produced are named mh_ess-sequence_prefix-mapping_parameters_gene_tas_m_parameter.csv where sequence_prefix is the basename() of the input sequence file, mapping_parameters are a string describing the bowtie mapping used, and m_parameter is usually one of 1,2,4,8,16,32 and defines the lower limit of read depth to be considered useful by the mh_ess package. Thus, before using this, one may want to look at the result from tnseq_saturation() to see if there is a most-appropriate m_parameter. I think I should figure out a heuristic to choose the m, but I am not sure what it would be, perhaps the median of the hits summary?

Usage

plot_essentiality(
  file,
  order_by = "posterior_zbar",
  keep_esses = FALSE,
  min_sig = 0.0371,
  max_sig = 0.9902
)

Arguments

file	Result from the DeJesus essentiality package. I think this has been effectively replaced by their TRANSIT package.
order_by	What column to use when ordering the data?
keep_esses	Keep entries in the data which are 'S' meaning insufficient evidence.
min_sig	Minimal value below which a gene is deemed non-essential and above which it is uncertain.
max_sig	Maximum value above which a gene is deemed essential and below which it is uncertain.

Value

A couple of plots

See Also

[ggplot2]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.