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) | 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) in six rings, one per reading frame | 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 |