Plot-Trait-Attribute: Plot Trait Attribute

In Jorisvansteenbrugge/TcT: Trait-based Comparative Transcriptomics

Plot Trait Attribute

Description

Convert a list with trait attributes to a matrix where each collumn is a trait attribute and each row a genome. Presence or absence is indicated with either a zero (0) or one (1).

Plot the expression profile for all genomes expressing that attribute. For each annotation a separate plot is created where the thick black line represents the mean expression of all genomes with that annotation. The dashed blue and red lines represent the mean + 0.5*sd and the mean - 0.5 * sd, respectively.

Usage

Traitattributes_To_Sbsmatrix(trait.attributes, genomes)

Plot_Trait_Attribute_Expression(
  trait.attribute = "M00793_1",
  trait.attributes.pruned,
  RNAseq.data
)

Arguments

trait.attributes	The full list of all trait attributes
genomes	A vector containing the names of all genomes present in the sample.
trait.attribute	The name of the trait attribute (as character string)
RNAseq.data	Collection of multple components, include RNA seq data, annotations, etc. See Pre_process_input for the full list.

Author(s)

JJM van Steenbrugge

JJM van Steenbrugge

Jorisvansteenbrugge/TcT documentation built on Sept. 26, 2022, 6:50 a.m.