Table 1 DensityMap options

-i

--input

string

GFF file name

-re

--region_file

string

A BED file describing sequence regions to plot.

It allow to plot specific regions and not the whole seq.

Example of file content:

2L[TAB]100000[TAB]200000

2R[TAB]300000[TAB]450000

-o

--output_img_name

string

output image name

-ty

--type_to_draw

string

Type (column 3 of GFF) to draw, strand(s) to plot and colour scale to use

Type: Match, gene, CDS, etc.

Strand:

- - > strand – (1 Density Map (or DM))

+ − > strand + (1 DM)

both - > strand - and strand + (2 DM)

fused - > Combination of strand - and strand + (1 DM)

all - > strand - and strand + and fused (3 DM)

Format: “Type1 = Strand = colour_scale”

i.e.: “match = all = 7;gene = both = 4;CDS = fused = 10”

-for

--force

none

Automatically answers yes to picture size validation

-v

--verbose

none

Activate verbose

-h

--help

none

Print help

-c

--colour_scale

integer

Number of the colour scale to use

-sc

--scale_factor

integer

Window length (in base pairs) to use

-a

--auto_scale_factor

integer

Maximum picture height in pixels

-ro

--rounding_method

string

Rounding densities with floor or ceiling

-gc

--gc

integer

Colour scale number for density map of the GC % of chromosome,

Requires the presence of the sequence in ##FASTA section of the GFF file

-ti

--title

string

Picture title

-w

--win_size

integer

Picture height in pixels

-sh

--show_scale

integer

Draw scale, with the integer indicating the maximum number of ticks to print on the scale

-str_w

--strand_width

integer

Strand width in pixels

-str_s

--strand_space

integer

Space between strands in pixels

-sp

--space_chr

Integer

Space between chromosomes

-lm

--lmargin

integer

Left margin in pixels

-rm

--rmargin

integer

Right margin in pixels

-tm

--tmargin

integer

Top margin in pixels

-bm

--bmargin

integer

Bottom margin in pixels

-ba

--background

integer

Picture background colour

-la

--label_strand_rotation

integer

Rotation (in degrees) of strand label

-ft_f

--ft_family

string

Text font

-ft_s

--ft_size

integer

Font size