Retain

Retain is show subgenomes in gene retention or genome fractionation.

Parameters

Parameters	Standards and instructions
alignment	Type:file | Default: - Output result of parameter a
colors	Type: { color1,color2,color3,– } Default: red,blue,green Set multiple sets of colors based on grouping, split with a comma.
refgenome	Type: str | Default: - A short handbook of reference species.
figsize	Type: int,int | Default: 10,10 Control the proportion of the size of the saved picture.
step	type: int | Default: 50 The size of the sliding window.
ylabel	Type: str | Default: none The y-axis label of the picture.
savefile	Type:file | Default: - Results of the drawing.
savefig	Type: {*. png,*. pdf, *. svg} | Default: *. png Save pictures support png, pdf, svg formats.

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

[retain]
alignment = alignment file
gff = gff file
colors = red,blue,green
refgenome = shorthand
figsize = 10,12
step = 50
ylabel = y label
savefile = retain file
savefig = result

Quick start

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

Example

The original results are easily accessible at wgdi-example