Customization Keys

The following keys can be used with the '--custom' option, which can be used with the cgview_comparison_tool.pl script and with the wrapper scripts build_blast_atlas.sh and build_blast_atlas_all_vs_all.sh. The values used must be consistent with those given below. For example, 'true' cannot be used when 'T' is expected. Colour values are given as rgb strings such as 'rgb(0,0,0)'.

When using the the '--custom' option with cgview_comparison_tool.pl, use quotes around values that contain spaces, as in this example:

cgview_comparison_tool.pl -p xylanase --custom featureOpacity=1 labelFontSize=50 title='some title'

When using the the '--custom' option with build_blast_atlas.sh or build_blast_atlas_all_vs_all.sh, use double quotes around the text passed to '--custom' and use single quotes around values containing spaces, as in this example:

  build_blast_atlas.sh -p AC_000022 -x --custom "title='Rattus rat' global_label=T legend=F use_opacity=F backboneRadius=4200"

Key Description Value
arrowheadLength Length of arrowheads used for genes and ORFs Real
average Plot base composition values as deviation from average T/F
atColorNeg Colour of AT content plot when low Colour
atColorPos Colour of AT content plot when high Colour
at_content Show AT content plot T/F
atSkewColorNeg Colour of AT skew plot when low Colour
atSkewColorPos Colour of AT skew plot when high Colour
at_skew Show AT skew plot T/F
backboneColor Colour of backbone circle Colour
backboneRadius Radius of backbone circle Real
backboneThickness Thickness of backbone circle Real
backgroundColor Colour of the background Colour
blast_divider_ruler Draw thicker divider rings around every tenth BLAST result and use a different colour (blastRulerColor). In addition, number the BLAST entries in the BLAST legend. Note that draw_divider_rings must be 'T' for the rings to be drawn T/F
blastRulerColor Colour of BLAST ruler rings (see blast_divider_ruler) Colour
borderColor Colour of border around map Colour
combined_orfs Draw ORFs in two rings (forward and reverse) instead of six T/F
details Show legend giving accession and sequence length T/F
draw_divider_rings Draw thin rings between BLAST rings and other rings T/F
featureOpacity Opacity used when drawing features Real between 0 and 1
featureOpacityOther Opacity used when drawing features of type other Real between 0 and 1
featureSlotSpacing Spacing between rings Real
featureThickness Thickness of feature rings Real
featureThicknessPlot Thickness of plots like GC content Real
feature_labels Label features from reference sequence GenBank file T/F
gcColorNeg Colour of GC content plot when low Colour
gcColorPos Colour of GC content plot when high Colour
gc_content Show GC content plot T/F
gcSkewColorNeg Colour of GC skew plot when low Colour
gcSkewColorPos Colour of GC skew plot when high Colour
gc_skew Show GC skew plot T/F
gene_decoration Whether to draw reference sequence features as arrows or arcs arrow/arc
gene_labels Label items read from 'features' or 'analysis' directories T/F
global_label Allow labels on zoomed maps (auto) all maps (T) or no maps (F) auto/T/F
height Height of the image in pixels Integer
hit_labels Label BLAST hits T/F
labelFontSize Size of font used for feature labels Integer
labelPlacementQuality Quality of label arrangement good/better/best
labelLineLength Starting length of lines running to feature labels Real
labelLineThickness Thickness of lines running to feature labels Real
legend Show legend for features T/F
legendFontSize Size of font used for legends Integer
orf_labels Label ORFs T/F
maxLabelLength Maximum number of letters shown in feature labels Integer
maxLegendLength Maximum number of letters shown in legends Integer
maxTitleLength Maximum number of letters shown in map title Integer
minimumFeatureLength Smallest glyph size used for features Real
moveInnerLabelsToOuter Move labels from inside of backbone to outside when labels clash true/false
orfColor Colour used for ORFs Colour
orfs Draw open reading frames (ORFs) T/F
orf_size Number of codons required to be an ORF Integer
otherColor Colour used for other features Colour
parse_reading_frame Subdivide each BLAST ring into six based on query reading frame T/F
proteinColor Colour used for CDS features Colour
reading_frames Draw start and stop codons T/F
rRNAColor Colour used for rRNA features Colour
rulerFontColor Colour of position number text Colour
rulerFontSize Size of font used for position numbers Integer
rulerPadding Space between innermost circle and position numbers Real
scale Scale base composition plots so that all space is used T/F
scale_blast Draw BLAST hits with height proportional to percent identity T/F
show_contigs Stagger divider rings to show the boundaries of contigs in sequences consisting of multiple contigs T/F
show_sequence_features Draw features from reference sequence GenBank file T/F
show_queries Show positions of the BLAST queries T/F
startColor Colour used for start codons Colour
starts Codons counting as start codons String like atg|ttg|att|gtg|ctg
step Sliding window step for base composition plots Integer
stopColor Colour used for stop codons Colour
stops Codons counting as stop codons String like taa|tag|tga
title Map title String
titleFontSize Size of font used in title at bottom Integer
tickColor Colour of tickmarks Colour
tickLength Length of tickmarks Real
tickThickness Thickness of tickmarks Real
tick_density Density of tickmarks Real between 0 and 1
tRNAColor Colour used for tRNA features Colour
useInnerLabels Allow feature labels on inside of backbone circle true/false
use_opacity Draw BLAST hits with partial opacity T/F
width Width of the image in pixels Integer
window Sliding window size for base composition plots Integer
_cct_blast_thickness Thickness of BLAST rings when '-cct' option used Real
_cct_blast_opacity Opacity of BLAST rings when '-cct' option used Real