Dotplot

Dotplot shows homologous gene dotplot.

Parameters

Parameters	Standards and instructions
blast_reverse	Type: bool | Default: false The first two columns of the blast result swap positions.
multiple	Type: int | Default: 1 The best number of homologous genes shown with red dots.
score	Type: int | Default: 100 Score value in blast result.
evalue	Type: float | Default: 1e-5 Evalue value in blast result.
repeat_number	Type: int | Default: 10 The maximum number of homologous genes is allowed to remove more than part of the population.
position	Type: {order, start , end } | Default: order The position of a gene corresponds to the gff file.
ancestor_left	Type: file | Default: none The ancestral chromosome region of the species on the left of dotplot.
ancestor_top	Type: file | Default: none The ancestral chromosome region of the species on the top of dotplot.
markersize	Type: float | Default: 0.5 The size of the point in the plot.
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 -d help >> total.conf Take out the parameter file.

[dotplot]
blast = blast file
blast_reverse = false
gff1 =  gff1 file
gff2 =  gff2 file
lens1 = lens1 file
lens2 = lens2 file
genome1_name =  Genome1 name
genome2_name =  Genome2 name
multiple  = 1
score = 100
evalue = 1e-5
repeat_number = 10
position = order
ancestor_left = none
ancestor_top = none
markersize = 0.5
figsize = 10,10
savefig = savefile(.png,.pdf)

Quick start

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

Example

The original results are easily accessible at wgdi-example