Customization Keys

The following keys can be used with the '--custom' option, which can be used with the script and with the wrapper scripts and 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)'.

Key Description Value
arrowheadLengthLength of arrowheads used for genes and ORFsReal
averagePlot base composition values as deviation from averageT/F
atColorNegColour of AT content plot when lowColour
atColorPosColour of AT content plot when highColour
at_contentShow AT content plotT/F
atSkewColorNegColour of AT skew plot when lowColour
atSkewColorPosColour of AT skew plot when highColour
at_skewShow AT skew plotT/F
backboneColorColour of backbone circleColour
backboneRadiusRadius of backbone circleReal
backboneThicknessThickness of backbone circleReal
backgroundColorColour of the backgroundColour
blast_divider_rulerDraw 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 drawnT/F
blastRulerColorColour of BLAST ruler rings (see blast_divider_ruler)Colour
borderColorColour of border around mapColour
combined_orfsDraw ORFs in two rings (forward and reverse) instead of sixT/F
detailsShow legend giving accession and sequence lengthT/F
draw_divider_ringsDraw thin rings between BLAST rings and other ringsT/F
featureOpacityOpacity used when drawing featuresReal between 0 and 1
featureOpacityOtherOpacity used when drawing features of type otherReal between 0 and 1
featureSlotSpacingSpacing between ringsReal
featureThicknessThickness of feature ringsReal
featureThicknessPlotThickness of plots like GC contentReal
feature_labelsLabel features from reference sequence GenBank fileT/F
gcColorNegColour of GC content plot when lowColour
gcColorPosColour of GC content plot when highColour
gc_contentShow GC content plotT/F
gcSkewColorNegColour of GC skew plot when lowColour
gcSkewColorPosColour of GC skew plot when highColour
gc_skewShow GC skew plotT/F
gene_decorationWhether to draw reference sequence features as arrows or arcsarrow/arc
gene_labelsLabel items read from 'features' or 'analysis' directoriesT/F
global_labelAllow labels on zoomed maps (auto) all maps (T) or no maps (F)auto/T/F
heightHeight of the image in pixelsInteger
hit_labelsLabel BLAST hitsT/F
labelFontSizeSize of font used for feature labelsInteger
labelPlacementQualityQuality of label arrangementgood/better/best
labelLineLengthStarting length of lines running to feature labelsReal
labelLineThicknessThickness of lines running to feature labelsReal
legendShow legend for featuresT/F
legendFontSizeSize of font used for legendsInteger
orf_labelsLabel ORFsT/F
maxLabelLengthMaximum number of letters shown in feature labelsInteger
maxLegendLengthMaximum number of letters shown in legendsInteger
maxTitleLengthMaximum number of letters shown in map titleInteger
minimumFeatureLengthSmallest glyph size used for featuresReal
moveInnerLabelsToOuterMove labels from inside of backbone to outside when labels clashtrue/false
orfColorColour used for ORFsColour
orfsDraw open reading frames (ORFs)T/F
orf_sizeNumber of codons required to be an ORFInteger
otherColorColour used for other featuresColour
parse_reading_frameSubdivide each BLAST ring into six based on query reading frameT/F
proteinColorColour used for CDS featuresColour
reading_framesDraw start and stop codonsT/F
rRNAColorColour used for rRNA featuresColour
rulerFontColorColour of position number textColour
rulerFontSizeSize of font used for position numbersInteger
rulerPaddingSpace between innermost circle and position numbersReal
scaleScale base composition plots so that all space is usedT/F
scale_blastDraw BLAST hits with height proportional to percent identityT/F
show_sequence_featuresDraw features from reference sequence GenBank fileT/F
show_queriesShow positions of the BLAST queriesT/F
startColorColour used for start codonsColour
startsCodons counting as start codonsString like atg|ttg|att|gtg|ctg
stepSliding window step for base composition plotsInteger
stopColorColour used for stop codonsColour
stopsCodons counting as stop codonsString like taa|tag|tga
titleMap titleString
titleFontSizeSize of font used in title at bottomInteger
tickColorColour of tickmarksColour
tickLengthLength of tickmarksReal
tickThicknessThickness of tickmarksReal
tick_densityDensity of tickmarksReal between 0 and 1
tRNAColorColour used for tRNA featuresColour
useInnerLabelsAllow feature labels on inside of backbone circletrue/false
use_opacityDraw BLAST hits with partial opacityT/F
widthWidth of the image in pixelsInteger
windowSliding window size for base composition plotsInteger
_cct_blast_thicknessThickness of BLAST rings when '-cct' option usedReal
_cct_blast_opacityOpacity of BLAST rings when '-cct' option usedReal