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Table 1 DensityMap options

From: DensityMap: a genome viewer for illustrating the densities of features

Short Long Type Description
Mandatory 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:
-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 – (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”
Generic options
-for --force none Automatically answers yes to picture size validation
-v --verbose none Activate verbose
-h --help none Print help
Density options
-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
Graphical options
-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