Question: SeqPattern plotPatternOccurrenceAverage problem
0
gravatar for elisheva.h02
17 months ago by
elisheva.h020 wrote:

Hi!

I am trying to plot average profile of dinucleotides frequency in human genes.

I am Using SeqPattern package for it, but when I am trying to add a y limit to the function plotPatternOccurrenceAverage I get an error.

Is there any way to fix this problem?

This is my code:

library(seqPattern)
library(BSgenome.Hsapiens.UCSC.hg19)
#--------------
#Genes
#--------------
#Read the TSS bed file.
HumanTSS <- read.delim(path,header = TRUE)
# create GRanges of dominant TSS position
HumanPromotersTSS <- GRanges(seqnames = HumanTSS$chr,ranges = IRanges(start = HumanTSS$dominantTSS,end = HumanTSS$dominantTSS),
                                 strand = HumanTSS$strand,interquantileWidth = NULL,seqlengths = seqlengths(Hsapiens))
# get regions flanking TSS - 3,000 bp upstream and 3,000 bp downstream.
HumanPromotersTSSflank <- promoters(HumanPromotersTSS, upstream = 3000,downstream = 10000)
#obtain genomic sequence of flanking regions
HumanPromotersTSSflankSeq <- getSeq(Hsapiens, HumanPromotersTSSflank)

op <- par(mar = c(7,7,4,2) + 0.1)
plotPatternOccurrenceAverage(regionsSeq = HumanPromotersTSSflankSeq,xLabel = "", yLabel = "",
                             patterns = c("C","G"), flankUp = 3000, flankDown = 10000,
                             smoothingWindow = 10, color = c("goldenrod","darkgreen"), xaxt='n',plotLegend = FALSE,cex.axis=1.5)
axis(1,at=c(-3000,0,3000,10000),labels=c("-3Kb","TSS","3Kb","10Kb"),cex.axis=1.5)
title(xlab="Relative distance from TSS",cex.lab=2, line = 4)
title(ylab = "Relative G frequency", cex.lab=2, line = 4)

When I tried to add y limit to the plotPatternOccurrenceAverage function like

ylim = c(0.05,0.35)

I got this error:

Error in plot.default(1, 1, xlim = c(-flankUp, flankDown), ylim = c(0,  : 
  formal argument "ylim" matched by multiple actual arguments

This is the session info:

R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

attached base packages:
 parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.2                  
rtracklayer_1.36.6                seqPattern_1.8.0                 
Biostrings_2.44.2                 XVector_0.16.0                   
GenomicRanges_1.28.6              GenomeInfoDb_1.12.3              
IRanges_2.10.5                    S4Vectors_0.14.7                 
BiocGenerics_0.22.1              

loaded via a namespace (and not attached):
magrittr_1.5               GenomicAlignments_1.12.2   zlibbioc_1.22.0           
BiocParallel_1.10.1        lattice_0.20-35            R6_2.2.2                  
rlang_0.1.6                stringr_1.2.0              httr_1.3.1                
tools_3.4.0                grid_3.4.0                 SummarizedExperiment_1.6.5
Biobase_2.36.2             plotrix_3.7                KernSmooth_2.23-15        
matrixStats_0.52.2         yaml_2.1.16                digest_0.6.13             
Matrix_1.2-9               GenomeInfoDbData_0.99.0    bitops_1.0-6              
RCurl_1.95-4.9             testthat_2.0.0             DelayedArray_0.2.7        
stringi_1.1.6              compiler_3.4.0             Rsamtools_1.28.0          
XML_3.98-1.9               swirl_2.4.3 

 

bug seqpattern • 312 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by elisheva.h020
Please include the code and output as well as `sessionInfo()`
ADD REPLYlink written 17 months ago by shepherl ♦♦ 1.7k

I edited my post

ADD REPLYlink written 17 months ago by elisheva.h020
1

In the internal code for this plotting function the ylim was hard coded by the maintainer. In its current state there is not an easy way around this. I would suggest emailing the maintainer directly to point out the potential bug. Maintainer: Vanja Haberle <vanja.haberle@gmail.com>

ADD REPLYlink written 17 months ago by shepherl ♦♦ 1.7k
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