kznfsComplexHeatmap: Use ComplexHeatmap to visualize KZNFs data from TEKRABber...

In ferygood/twice: A collections of useful functions to analyze transcription factors and transposable elements data

Use ComplexHeatmap to visualize KZNFs data from TEKRABber result

Description

This function use ComplexHeatmap::Heatmap() to visualize KZNFs data generated from using TEKRABber. First it will load the built-in hmKZNFs337 and filter the dataframe. The dataframe is the file with extension geneDESeq2norm.csv from TEKRABber. You can specified how many of the KZNFs you want to visualize. The default is showing the top 40 KZNFs with the highest row means among all samples. If you face an error with could not find function "unit", you need to load the ComplexHeatmap library to your workspace.

Usage

kznfsComplexHeatmap(
  df,
  top = 40,
  species = "hsapiens",
  fileName = NULL,
  orderMean = FALSE,
  speciesAnnot = NULL
)

Arguments

df	a TEKRABber geneDESeq2norm table
top	a numeric value to show top number of genes in heatmap
species	indicate the species name to convert ID
fileName	the name for saving pdf file (if specified)
orderMean	specify if you want to order the rows based on row means
speciesAnnot	a vector containing species information if you want to add top annotation on your heatmap

Value

a ComplexHeatmap heatmap (Formal class Heatmap)

Examples

data(hmchimpGene)
annot <- c("Hs", "Hs", "Hs", "Pt", "Pt", "Pt")
kznfsComplexHeatmap(hmchimpGene, top=40, species="hsapiens",
                    speciesAnnot=annot)

ferygood/twice documentation built on May 4, 2023, 11:26 p.m.