NAME
last-dotplot - make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format
SYNOPSIS
last-dotplot --help
last-dotplot [options] maf-or-psl-or-tab-alignments
last-dotplot [options] maf-or-psl-or-tab-alignments dotplot.png|gif|...
DESCRIPTION
Draw a dotplot of pair-wise sequence alignments.
OPTIONS
- -h, --help
-
show this help message and exit
- -v, --verbose
-
show progress messages & data about the plot
- -x INT, --width=INT
-
maximum width in pixels (default: 1000)
- -y INT, --height=INT
-
maximum height in pixels (default: 1000)
- -m M, --maxseqs=M
-
maximum number of horizontal or vertical sequences (default=100)
- -1 PATTERN, --seq1=PATTERN
-
which sequences to show from the 1st genome
- -2 PATTERN, --seq2=PATTERN
-
which sequences to show from the 2nd genome
- --alignments=FILE
-
secondary alignments
- --sort1=N
-
genome1 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1)
- --sort2=N
-
genome2 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1)
- --strands1=N
-
genome1 sequence orientation: 0=forward orientation, 1=alignment orientation (default=0)
- --strands2=N
-
genome2 sequence orientation: 0=forward orientation, 1=alignment orientation (default=0)
- --max-gap1=FRAC
-
maximum unaligned (end,mid) gap in genome1: fraction of aligned length (default=1,4)
- --max-gap2=FRAC
-
maximum unaligned (end,mid) gap in genome2: fraction of aligned length (default=1,4)
- --pad=FRAC
-
pad length when cutting unaligned gaps: fraction of aligned length (default=0.04)
- -j N, --join=N
-
join: 0=nothing, 1=alignments adjacent in genome1, 2=alignments adjacent in genome2 (default=0)
- --border-pixels=INT
-
number of pixels between sequences (default=1)
- -a FILE, --bed1=FILE, --rmsk1=FILE, --genePred1=FILE, --gap1=FILE
-
read genome1 annotations
- -b FILE, --bed2=FILE, --rmsk2=FILE, --genePred2=FILE, --gap2=FILE
-
read genome2 annotations
-
Text options:
- -f FILE, --fontfile=FILE
-
TrueType or OpenType font file
- -s SIZE, --fontsize=SIZE
-
TrueType or OpenType font size (default: 14)
- --labels1=N
-
genome1 labels: 0=name, 1=name:length, 2=name:start:length, 3=name:start-end (default=0)
- --labels2=N
-
genome2 labels: 0=name, 1=name:length, 2=name:start:length, 3=name:start-end (default=0)
- --rot1=ROT
-
text rotation for the 1st genome (default=h)
- --rot2=ROT
-
text rotation for the 2nd genome (default=v)
-
Color options:
- -c COLOR, --forwardcolor=COLOR
-
color for forward alignments (default: red)
- -r COLOR, --reversecolor=COLOR
-
color for reverse alignments (default: blue)
- --border-color=COLOR
-
color for pixels between sequences (default=black)
- --margin-color=COLOR
-
margin color
- --exon-color=COLOR
-
color for exons (default=PaleGreen)
- --cds-color=COLOR
-
color for protein-coding regions (default=LimeGreen)
- --bridged-color=COLOR
-
color for bridged gaps (default: yellow)
- --unbridged-color=COLOR
-
color for unbridged gaps (default: orange)