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The track features (bars) do not appear on the plot #22

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khash79 opened this issue Apr 14, 2022 · 0 comments
Open

The track features (bars) do not appear on the plot #22

khash79 opened this issue Apr 14, 2022 · 0 comments

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@khash79
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khash79 commented Apr 14, 2022

Hi

im trying to use your package to illustrate a feature on genome. i defined the my-genome as such ;

my_genome= c("chr1"= 24891,"chr2"= 24186, "chr3"= 19797, "chr4"= 18995, "chr5"= 18126, "chr6"= 17058 , "chr7"= 15903, "chr8"= 14506, "chr9"= 13788, "chr10"= 13356, "chr11"= 13439, "chr12"= 13322, "chr13"= 11432, "chr14"= 10553, "chr15"= 10181, "chr16"= 9006, "chr17"= 8308, "chr18"= 8017, "chr19"= 5857, "chr20"= 6426, "chr21"= 4664, "chr22"= 5074, "chrX"= 1550, "chrY"= 2058)

tried to define the track for the following df using depletion variable

str(df)
'data.frame': 15987 obs. of 6 variables:
$ Gene : chr "SAMD11" "NOC2L" "KLHL17" "PLEKHN1" ...
$ Chr : chr "chr1" "chr1" "chr1" "chr1" ...
$ Start : num 92.5 94.4 96.1 96.6 99.9 ...
$ End : num 92.5 94.5 96.1 96.7 99.9 ...
$ cnv : num -0.877 -0.566 -0.787 -0.961 -0.486 ...
$ depletion: num 0 2.9 0 0 0.11 0 0 0 0 0.12 ...

the track making is as the following ;

track = BioCircosTracklist()
track= track+BioCircosBarTrack(trackname = "bars" , chromosomes = df$Chr , starts = df$Start ,ends= df$End ,values =df2$depletion ,color = "red", range = c(0,4.5))
track= track + BioCircosBackgroundTrack("bars_background" )

however, when i run the code;
BioCircos(genome = as.list(my_genome), genomeFillColor = "Oranges",
genomeTicksDisplay = F, tracklist = track, genomeTicksTextSize = 2)

i dont get any bars on the track. suprisingly , however, when i just type in some of the values as a test bars do appear.

Can you please help out with this and let me know what im doing wrong? Thanks

Best
khash

p.s. tried naming the numerics for value by chr but still no luck .

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