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 .
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 .