visu.m.s.enrichment: Plot enrichment by condition and comparisons.

In carinelegrand/RiboVIEW: Visualization, Quality and Statistics for Ribosome Profiling

Description

visu.m.s.enrichmnt This function takes a list of samples and experimental conditions in input and generates plots for codon enrichment of all replicates of the same condition, and for each comparison between conditions.

Usage

visu.m.s.enrichmnt(XP.conditions, XP.names, pathout)

Arguments

XP.conditions	Vector of experimental conditions for each sample
XP.names	Vector of names for each sample
pathout	Address where output files will be written

Value

This function returns a list containing the following :

plot.enrich

Address of the png plot file for codon enrichment for each condition across replicates

plot.compar

Address of one of the png plot file for codon enrichment comparison between two different experimental conditions

Examples

# Sequenced reads aligned to mRNA (and containing no rRNA, depleted previously),
#   in bam format
readsBAM.1.1  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond1-Rep1.bam",sep="")
readsBAM.1.2  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond1-Rep2.bam",sep="")
readsBAM.1.3  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond1-Rep3.bam",sep="")
readsBAM.2.1  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond2-Rep1.bam",sep="")
readsBAM.2.2  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond2-Rep2.bam",sep="")
readsBAM.2.3  <- paste(system.file(package="RiboVIEW", mustWork = TRUE), 
                                              "/extdata/Cond2-Rep3.bam",sep="")

list.bam <- list(readsBAM.1.1, readsBAM.1.2, readsBAM.1.3, 
                 readsBAM.2.1, readsBAM.2.2, readsBAM.2.3)


#
## Experimental conditions, in text and as indicators :
#    0 for control
#    1 for a condition, treatment, case, etc...
#    2, 3, etc. for further conditions

XP.conditions   <- c("cond1","cond1","cond1","cond2", "cond2","cond2")
XP.conditions.i <- c( 1,1,1,2,2,2)
XP.names        <- c("C1.R1", "C1.R2", "C1.R3", 
                     "C2.R1", "C2.R2", "C2.R3")

#
## Reference annotation for mRNAs' CDS.
#

refCDS <- paste(system.file(package="RiboVIEW", mustWork = TRUE), "/extdata/synth.tsv", sep="")
# Note : CDS annotation can be obtained from a GTF file, 
#        using gtf2table(my-gtf-file, outfile = my-cds-file)
#        (for example GTF file as provided by Ensembl.org work well with gtf2table)

#
## Reference sequences for mRNAs.
#

refFASTA <- paste(system.file(package="RiboVIEW", mustWork = TRUE), "/extdata/synth.fasta", sep="")

#
## Work and output folder.
#

pathout  <-  paste(tempdir(),"/", sep="")
  ## !! This is a temporary directory, which will be erased when you leave R !!
  ##   For your own analyses you would probably prefer to point to a permanent repository :
  #      pathout <- /home/me/address-to-my-output-repository/ # Define address, 
  #                                                   #including a final slash.
  #      system(paste('mkdir',pathout)) # Create folder at said address.
  #      setwd(pathout)  # Go to this directory. This is useful if you want to 
  #                                         #save additional tables or figures.

# 
## A-site coverage periodicity by length
#

periodicity(list.bam, refCDS, refFASTA, pathout, XP.names, versionStrip = FALSE)

# 
## Select footprint length with sufficient periodicity
#

attach(listminmax <- select.FPlen(list.bam, pathout, XP.names))

#
## Codon occupancy, codon enrichment.
# 

enrichmentNoccupancy(list.bam, refCDS, refFASTA, mini, maxi, XP.names,  
                       pathout, versionStrip = FALSE)
 
#
## Visualisation.
#

generate.m.s(XP.conditions, XP.names, pathout, B=1000)

visu.m.s.enrichmnt.res <- visu.m.s.enrichmnt(XP.conditions, XP.names, pathout)
visu.m.s.enrichmnt.res

visu.tracks.res <- visu.tracks(XP.conditions, XP.names, pathout, refCDS, 
                               mRNA="random", 
                               codon.labels=FALSE, codon.col="darkslateblue")
visu.tracks.res

Venn.all.res <- Venn.all(XP.names, pathout)
Venn.all.res

enricht.aroundA.res <- enricht.aroundA(XP.conditions, 
  XP.names, pathout)
enricht.aroundA.res

carinelegrand/RiboVIEW documentation built on July 17, 2020, 3:02 p.m.