Circos

Circos is a simple way to run circos.

Parameters

Parameters	Standards and instructions
alignment	Type:file | Default: - Output result of parameter a
radius	Type: float | Default: 0.2 Radius, value between 0-1.
angle_gap	Type: float | Default: 0.05 Gap between chromosomes.
ring_width	Type: float | Default: 0.015 The width of the ring.
colors	Type:{chr1:color1,chr2:color2,} Default: 1:red,2:orange,3:blue,4:cyan,5:green Set multiple sets of colors based on grouping, split with a comma.
position	Type: {order, start , end } | Default: order The position of a gene corresponds to the gff file.
chr_label	Type: str | Default: - A shorthand for chromosomes.
column_names	Type: str | Default: - Column markers of the alignment file.
ancestor_location	Type: file | Default: none The ancestral chromosome region of the species.
alignment	Type:file | Default: - Alignment of hierarchical and event-related gene collinearity.
figsize	Type: int,int | Default: 10,10 Control the proportion of the size of the saved picture.
savefig	Type: {*. png,*. pdf, *. svg} | Default: *. png Save pictures support png, pdf, svg formats.

Use command to enter the folder wgdi -ci ? >> total.conf Take out the parameter file.

[circos]
gff =  gff file
lens = lens file
radius = 0.2
angle_gap = 0.05
ring_width = 0.015
colors  = 1:c,2:m,3:blue,4:gold,5:red,6:lawngreen,7:darkgreen,8:k,9:darkred,10:gray
alignment = alignment file
chr_label = chr
ancestor_location = ancestor file
ancestor = alignment file
figsize = 10,10
label_size = 9
columns_name = 1,2,3,4,5
savefig = result(.png, .pdf, .svg)

Quick start

After the parameters are modified properly, then run wgdi -ci total.conf

Example