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general
Andrew Wilkey edited this page Apr 9, 2019
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The general section describes how to draw the base items of CViT, title, ruler, and any data that has the type column (3rd) as chromosome
this is the only section that requires the third colum to be set as a specific value, and it is suggested in more
complicated CViT uses to use one gff file for these backbone values and use a second gff with all your other data.
| Option | Default | Description |
|---|---|---|
| title | none | Label for image. |
| title_height | 20 | Space allowance for title in pixels, can ignore if font face and size set |
| title_font_face | fontDefault | Font face to use for title, ignored if empty |
| title_font_size | 10 | Title font size in points, used only in conjunction with font_face |
| title_color | black | Title font color |
| title_location | none | Title location as x,y coords, ignored if missing |
| image_padding | 10 | preferred distance between image and ruler in px |
| border_color | black | Color of the border around the image |
A "chromosome" can be any sort of contiguous sequence: chromosome, arm, contig, BAC, et cetera.
| Option | Default | Description |
|---|---|---|
| chrom_width | 10 | Width of chromosome in px |
| fixed_chrom_spacing | 1 | (boolean) if 0, automatically attempt to fit all chromosomes in view window, otherwise use fixed values |
| chrom_spacing | 90 | Number of pixles between chromosomes |
| chrom_color | gray50 | (color) Fill color for the chromosome bar |
| chrom_border_color | black | Border color for the chromosome bar |
| chrom_font_face | fontDefault | Fontface to use for labels |
| chrom_font_size | 10 | Font size for chromosome labels in points. |
| chrom_label_color | gray50 | (color) Color of chromosome labels |
In addition the following options have been added from the legacy format:
| Option | Default | Description |
|---|---|---|
| chrom_padding_top | 50 | pixels between start of smallest chromosome and top of canvas |
| chrom_padding_bottom | 50 | pixles between stop of talles chromosome and bottom of canvas |
| chrom_border_size | 2 | width of chromosome border |
| Option | Default | Description |
|---|---|---|
| display_ruler | 1 | The ruler is a guide down either side of image showing units 0=none, 1=both, L=left side only, R=right side only |
| reverse_ruler | 0 | (boolean) 1 = ruler units run greatest to smallest |
| ruler_units | none | Ruler units (e.g. "cM, "kb") |
| ruler_min | 0 | minimum value on ruler, if > min chrom value, will be adjusted |
| ruler_max | 0 | Maximum value on ruler, if < max chrom value, will be adjusted |
| ruler_color | gray60 | (color) Color to use for the rulers and labels |
| ruler_font_face | fontDefault | Font face to use for ruler labels |
| ruler_font_size | 6 | Ruler font size in points, used only in conjuction with font_face |
| tick_line_width | 8 | length of ruler tick marks |
| tick_interval | 50000 | Ruler tick mark units in original chromosome units |
| minor_tick_divisions | 2 | Number of minor divisions per major tick (1 for none) |
class_colors has been depreciated, due to issues with reliable reproduction of images in an asynchronous environment.