plotMotifs {circRNAprofiler}R Documentation

Plot motifs analysis results

Description

The function plotMotifs() generates 2 bar charts showing the log2FC and the number of occurences of each motif found in the target sequences (e.g detected Vs randomly selected).

Usage

plotMotifs(mergedMotifsFTS, mergedMotifsBTS, log2FC = 1, nf1 = 1,
  nf2 = 1, df1Name = "foreground", df2Name = "background")

Arguments

mergedMotifsFTS

A data frame containing the number of occurences of each motif found in foreground target sequences (e.g from detected back-spliced junctions). It can be generated with the mergeMotifs.

mergedMotifsBTS

A data frame containing the number of occurences of each motif found in the background target sequences (e.g. from random back-spliced junctions). It can be generated with the mergeMotifs.

log2FC

An integer specifying the log2FC cut-off. Default value is 1.

nf1

An integer specifying the normalization factor for the first data frame mergedMotifsFTS. The occurrences of each motif are divided by nf1. The normalized values are then used for fold-change calculation. Set this to the number of target sequences (e.g from detected back-spliced junctions) where the motifs were extracted from. Default value is 1.

nf2

An integer specifying the normalization factor for the second data frame mergedMotifsBTS. The occurrences of each motif are divided by nf2. The normalized values are then used for fold-change calculation. Set this to the number of target sequences (e.g from random back-spliced junctions) where the motifs were extracted from. Default value is 1.

NOTE: By setting nf1 and nf2 equals to 1 the number of target sequences (e.g detected Vs randomly selected) where the motifs were extrated from, is supposed to be the same.

df1Name

A string specifying the name of the first data frame. This will be displayed in the legend of the plot. Deafult value is "foreground".

df2Name

A string specifying the name of the first data frame. This will be displayed in the legend of the plot. Deafult value is "background".

Value

A ggplot object.

Examples

# Load data frame containing detected back-spliced junctions
data("mergedBSJunctions")

# Load short version of the gencode v19 annotation file
data("gtf")

# Annotate the first back-spliced junctions
annotatedFBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)

# Get random back-spliced junctions
randomBSJunctions <- getRandomBSJunctions(gtf, n = 1, f = 10)

# Annotate random back-spliced junctions
annotatedBBSJs <- annotateBSJs(randomBSJunctions, gtf, isRandom = TRUE)

# Get genome
genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")

# Retrieve target sequences from detected back-spliced junctions
targetsFTS <- getSeqsFromGRs(
   annotatedFBSJs,
   genome,
   lIntron = 200,
   lExon = 10,
   type = "ie"
   )

# Retrieve target sequences from random back-spliced junctions
targetsBTS <- getSeqsFromGRs(
   annotatedBBSJs,
   genome,
   lIntron = 200,
   lExon = 10,
   type = "ie"
   )

# Get motifs
 motifsFTS <- getMotifs(
     targetsFTS,
     width = 6,
     species = "Hsapiens",
     rbp = TRUE,
     reverse = FALSE)

motifsBTS <- getMotifs(
     targetsBTS,
     width = 6,
     species = "Hsapiens",
     rbp = TRUE,
     reverse = FALSE)

# Merge motifs
 mergedMotifsFTS <- mergeMotifs(motifsFTS)
 mergedMotifsBTS <- mergeMotifs(motifsBTS)

# Plot
 p <- plotMotifs(
     mergedMotifsFTS,
     mergedMotifsBTS,
     log2FC = 2,
     nf1 = nrow(annotatedFBSJs),
     nf2 = nrow(annotatedBBSJs),
     df1Name = "foreground",
     df2Name = "background")


[Package circRNAprofiler version 1.0.0 Index]