Sushi package draws gene structure diagram
The plotGenes of the Sushi package can plot gene structures, such as the visualization of several transcriptome structures.
- bed format data frame
The structure is as follows
chrom start stop gene score strand1 chr15 73017309 73017438 COX5A . - chr15 72999672 72999836 COX5A . - chr15 73003042 73003164 COX5A . - chr15 73006160 73006281 COX5A . - chr15 73008510 73008626 COX5A . -
The structure is as follows
chrom start stop gene score strand type chr15 73062668 73062770 ENST00000362710 0.000000 -1 exon chr15 73097788 73097929 ENST00000361900 0.000000 1 exon chr15 73097264 73097365 ENST00000361900 0.000000 1 exon chr15 73095987 73096143 ENST00000361900 0.000000 1 exon chr15 73092071 73092199 ENST00000361900 0.000000 1 exon chr15 73091234 73091240 ENST00000361900 0.000000 1 exon chr15 73017309 73017408 ENST00000322347 31.488695 -1 exon chr15 73006160 73006281 ENST00000322347 31.488695 -1 exon
library('Sushi') # Load Sushi包 Sushi_data = data(package ='Sushi') # List Sushi own data data(list = Sushi_data$results[,3]) # Load data chrom = "chr15" chromstart = 72998000 chromend = 73020000 pg = plotGenes(Sushi_genes.bed,chrom,chromstart,chromend, types=Sushi_genes.bed$type,maxrows=1,bheight=0.2, plotgenetype="arrow",bentline=FALSE,labeloffset=.4, fontsize=1.2,arrowlength = 0.025,labeltext=TRUE) # Because our typse input is Sushi_genes.bed$type, which is actually NULL, the default "exon" will be used, and exon and utr are optional labelgenome( chrom, chromstart,chromend,n=3,scale="Mb") #Add genome coordinates
plotgenetype="box" can display the area whose type is exon and utr in the form of box
library('Sushi') # Load Sushi bag Sushi_data = data(package ='Sushi') # List Sushi's own data data(list = Sushi_data$results[,3]) # Load data chrom = "chr15" chromstart = 72965000 chromend = 72990000 pg = plotGenes(Sushi_transcripts.bed,chrom,chromstart,chromend , types = Sushi_transcripts.bed$type, colorby=log10(Sushi_transcripts.bed$score+0.001), colorbycol= SushiColors(5),colorbyrange=c(0,1.0), labeltext=TRUE,maxrows=50,height=0.4,plotgenetype="box") # colorby is the column that specifies the color change, and colorbycol is the color palette that specifies the color change labelgenome( chrom, chromstart,chromend,n=3,scale="Mb") #Add genome coordinates addlegend(pg[],palette=pg[],title="log10(FPKM)",side="right", bottominset=0.4,topinset=0,xoffset=-.035,labelside="left", width=0.025,title.offset=0.055) #Add legend
62 thoughts on “Sushi package draws gene structure diagram”
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