plotBed R data frame - last line plotted with line 1
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waqasnayab • 0
@waqasnayab-10130
Last seen 8.3 years ago

Hi,

I am using sushi package for visualizing genome data.

My data frame looks like this:

head (mydata):

         chrom start end     name score strand row 
1 COSN17118087    23  36  AP2D_f1     0      .   1
2 COSN17118087    15  34 BHE41_f1     0      .   2
3 COSN17118087     7  15  COT1_si     0      .   3
4 COSN17118087     6  15  COT2_f1     0      .   4
5 COSN17118087     6  25  HEN1_si     0      .   5
6 COSN17118087    21  29  HTF4_f1     0      .   6

tail (mydata):

          chrom start end     name score strand row
19 COSN17118087     6  22   THA_f2     0      .  18
20 COSN17118087     3  19   THB_do     0      .  19
21 COSN17118087     7  23   THB_do     0      .  19
22 COSN17118087     7  16   THB_f1     0      .  20
23 COSN17118087    21  30 TWST1_f1     0      .  21
24 COSN17118087    32  40  ZIC3_f1     0      .  22

My R code is:

mydata = read.table ("svlfctrs.bed" , header = T)

chrom = "COSN17118087"

> chromstart = 1

> chromend = 41

> mydata$color =maptocolors(mydata$row,col=SushiColors(6)) 

> plotBed(beddata = mydata,chrom = chrom, chromstart = chromstart,chromend =chromend, rownumber = mydata$row, type ="region", color=mydata$color,row="given",plotbg="grey95",rowlabels=unique(mydata$name),rowlabelcol=unique(mydata$color),rowlabelcex=0.75) 

> labelgenome(chrom,chromstart,chromend,n=10,scale="bp")

The problem is with the plot. http://s31.postimg.org/chblg444b/waq_biostr_sushi.png 

The data point of first line, that is, 1 COSN17118087 23 36 AP2D_f1 0 . 1 merges with the last data point of my data frame, that is, 24 COSN17118087 32 40 ZIC3_f1 0 . 22

Is there any way to solve the issue?

Thanks,

Waqas.

 

 

sushi plotBed data.frame • 1.2k views
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0
Entering edit mode
waqasnayab • 0
@waqasnayab-10130
Last seen 8.3 years ago

Hi,

I made it. There is no bug or any formatting issue in the plot. The problem is in my input (column no. 7 – row column). I gave the same numbering to two different transcription factors that’s why they overlapped. Everything sorted now.

Thanks for everyone,

Regards,

Waqas.

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