SmearPlot: Smear plot for Differentially Expressed genes and TFs

In cbiagii/pcitRif: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Smear plot for Differentially Expressed genes and TFs

Description

Generate an plot for Differentially Expressed (DE) genes and for specific TF that shows the relationship between log(baseMean) and Difference of Expression or log2FoldChange. This plot enables to visualize the distribution of DE genes and TF in both conditions.

Usage

SmearPlot(
  object,
  diffMethod,
  lfc = 1.5,
  conditions,
  TF = NULL,
  padjust = 0.05,
  label = FALSE,
  type = NULL
)

Arguments

object	CeTF class object resulted from runAnalysis function.
diffMethod	Method used to calculate Differentially Expressed (DE) genes (see expDiff).
lfc	logFoldChange module threshold to define a gene as differentially expressed (default: 1.5).
conditions	A vector of characters identifying the names of conditions (i.e. c('normal', 'tumoral')).
TF	Specify a single TF to be visualized for (used only if type argument equals TF).
padjust	Significance value to define a gene as differentially expressed in DESeq2 diffMethod option (default: 0.05).
label	If label is TRUE, shows the names of single TF and its respectives (default: FALSE).
type	Type of plot (DE or TF). If DE, will plot the smear plot for all differentally expressed genes and TFs for both conditions, and if TF, will plot the smear plot for a specific TF and their targets. targets for both conditions (default: FALSE).

Value

Returns an plot of log2(baseMean) by log2FoldChange or difference of expression for genes and TFs differentially expressed or for a single TF and its targets for both conditions.

Examples

# load the CeTF class object resulted from runAnalysis function
data(CeTFdemo)

#performing SmearPlot for DE genes and TFs
SmearPlot(object = CeTFdemo, 
          diffMethod = 'Reverter', 
          lfc = 1.5, 
          conditions = c('untrt', 'trt'), 
          type = 'DE')

#performing SmearPlot for DE genes and TFs
SmearPlot(object = CeTFdemo,
          diffMethod = 'Reverter',
          lfc = 1.5,
          conditions = c('untrt', 'trt'),
          TF = 'ENSG00000205189',
          label = FALSE, 
          type = 'TF')

cbiagii/pcitRif documentation built on Feb. 5, 2023, 9:03 p.m.