JCVI作图进阶系列（二）

local synteny plot, focus on gene-level show matching regions along with aligned gene models.

PS：第一步输入文件源自系列（一）的输出结果

一、准备工作

#Compute the layout for the gene-level matchings

python -m jcvi.compara.synteny mcscan grape.bed grape.peach.lifted.anchors --iter=1 -o grape.peach.i1.blocks

#Choose any arbitrary region to visualize

head -50 grape.peach.i1.blocks > blocks

#conbime *.bed(grape_peach.bed)

cat grape.bed peach.bed > grape_peach.bed

#make blocks.layout(blocks.layout)

# x,   y, rotation,   ha,     va,   color, ratio,            label
0.5, 0.6,        0, left, center,       m,     1,       grape Chr1
0.5, 0.4,        0, left, center, #fc8d62,     1, peach scaffold_1
# edges
e, 0, 1

二、作图

使用jcvi.graphics.synteny模块，尝试不同作图风格，结果见blocks.pdf

#default_style
python -m jcvi.graphics.synteny blocks grape_peach.bed blocks.layout --notex
#line_shadestyle
python -m jcvi.graphics.synteny blocks grape_peach.bed blocks.layout --shadestyle=line --notex
#arrow_glyphstyle
python -m jcvi.graphics.synteny blocks grape_peach.bed blocks.layout --glyphstyle=arrow --notex
#orthogroup_glyphcolor(同源块颜色对应)
python -m jcvi.graphics.synteny blocks grape_peach.bed blocks.layout --glyphcolor=orthogroup --notex
#show all gene_labels
python -m jcvi.graphics.synteny blocks grape_peach.bed blocks.layout --genelabelsize 6 --notex
#show a few gene_labels
python -m jcvi.graphics.synteny blocks grape_peach.bed blocks.layout --genelabelsize=10 --genelabels=GSVIVT01012244001,Prupe.1G289800.1,GSVIVT01012225001,Prupe.1G288000.1 --notex

三、结果

此处展示不同作图参数作图的结果blocks.pdf

#blocks1.pdf(default)