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Error in plotAvgProf.internal(): "please specify appropreate xcoordinations" #240

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Panzer-vor-08 opened this issue Sep 22, 2024 · 0 comments

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@Panzer-vor-08
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Panzer-vor-08 commented Sep 22, 2024

I am trying to draw density plot with ChIPseeker. Here's my code:

flag1 = readPeakFile("dTAG_rep2_peaks.narrowPeak")
txdb_mouse <- TxDb.Mmusculus.UCSC.mm10.knownGene
promoter = getPromoters(TxDb = txdb_mouse)
flag1_1 = annotatePeak(flag1, TxDb = txdb_mouse)
flag1_1 = as.GRanges(flag1_1)
flag1Matrix = getTagMatrix(flag1_1, upstream=5000, downstream=5000, 
                           #windows=getBioRegion(txdb_mouse),
                           windows=promoter,
                           type = 'body', by='gene'
                           )
tagHeatmap(flag1Matrix, xlim=c(-1000, 1000))
plotAvgProf(flag1Matrix, xlim=c(-2000, 2000))

When I run the function plogAvgProf, this is the output massage:

plotting figure...			 2024-09-22 9:08:07 
Error in plotAvgProf.internal(tagMatrix = tagMatrix, conf = conf, xlim = xlim,  : 
  please specify appropreate xcoordinations...

I tried several times, the error won't appear only when the xlim was set to c(-1000, 1000). c(-1001, 1001) and c(-999, 999) neither works.
I am plotting with windows R4.2.3, ChIPseeker version=1.34.1

This problem can be reproduced on my macair, with R4.4.1 and ChIPseeker version=1.40.0.

I am still confused by this problem and I am looking forward to your reply.

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