dotplot.template

################################################################################
# This is a template for a parameter file for running the R program dotplot.R,
# which makes dot plots of LCR data from an IGGPIPE LCRs_*.tsv output file.
# This file is configured to use the LCRs_*.tsv file produced as a result of
# running IGGPIPE using the test parameter file named allParameters.test.
# Therefore, you can test dotplot.R with this command:
#
#   Rscript code/R/dotplot.R dotplot.template
#
# To make your own dot plots, copy this file to another filename and edit it to
# set the parameters for your own dot plot.
################################################################################

# Many parameters come in pairs, one for the x-axis (first genome) and one for
# the y-axis (second genome).


# Path of the "LCRs_*.tsv" file to use as input for the dot plot.  This path
# should be specified relative to the main IGGPIPE directory, assuming that the
# dotplot.R program is run after changing to that directory.

LCR.file := "outTestHP11/LCRs_K11k2L100D10_2000.tsv"


# The two letters assigned to the two genomes that are to be plotted.  The data
# for the genome of the first letter specified is plotted on the x-axis and the
# second letter is for the y-axis.

PLOT.genomes := HP


# Path of the dot plot output file, which is a .png file.

PLOT.file := "outTestHP11/LCRs_K11k2L100D10_2000.dotplot.png"


# Names of .idlens files containing IDs and lengths of each sequence in each
# genome's FASTA file.  These files are made by IGGPIPE when it is run.  They
# can be found in the GenomeData subfolder within the output folder for that
# IGGPIPE run.  They are normally named "Genome_1.idlens", "Genome_2.idlens",
# "Genome_3.idlens", etc. for however many genomes there were.
X.idlens := "outTestHP11/GenomeData/Genome_1.idlens"
Y.idlens := "outTestHP11/GenomeData/Genome_2.idlens"


# Output file resolution in pixels.
PLOT.width := 2000
PLOT.height := 2000


# Plot margins in inches.
PLOT.margin.top := 0.5
PLOT.margin.bottom := 2.25
PLOT.margin.left := 2.25
PLOT.margin.right := 0.5


# Background color of dot plot, using color names from R ("white", "black", "blue",
# etc. or HTML #xxxxxx hex RGB colors such "#FF0080" or two additional hex digits
# specifying the alpha channel in addition to RGB (such as "#FF008055").
BKGD.color := black


# Foreground color for plotting things like axes and labels.
FGND.color := white


# Plot points (one at each common unique k-mer) or lines (connecting all
# common unique k-mers of an LCR).
PLOT.which := lines   # Else points


# Point size and line width, may be fractional.
POINT.size := 0.05
LINE.width := 2


# Point or line color, and amount of alpha channel (transparency) in the color,
# with 0 meaning completely transparent and 1 meaning completely solid.  As
# points or lines pile up on top of each other, the color gets less transparent.
PTLINE.color := white
PTLINE.alpha := 1


# If X.grid.lines.per.seqid/y is not 0, grid lines are drawn.  Each chromosome
# or sequence ID that is plotted (see X.PLOT.seqids/Y.PLOT.seqids below) has
# X.grid.lines.per.seqid/y grid lines drawn on it.  The lines are spaced evenly
# throughout the length of the chromosome.  If X.grid.lines.per.seqid/y is 1,
# the single grid line is placed at the center of each chromosome.  Otherwise,
# there will be one grid line at the start and one at the end of each chromosome,
# with the rest spaced evenly between.
# Also defined here is the grid line color and line width.
X.grid.lines.per.seqid := 8
Y.grid.lines.per.seqid := 8
GRID.line.color := gray
GRID.line.width := 1


# GRID label color, size, and x- and y- position.  For no grid labels, set
# GRID.label.size to 0.  Position is 0 for neutral, negative for inward, positive
# for outward.
X.grid.label.position := -3
Y.grid.label.position := -4
GRID.label.color := gray
GRID.label.size := 2

# Which sequence IDs should be plotted in each genome?  Leave these lists empty
# to plot ALL sequence IDs, otherwise list the sequence IDs with commas separating
# them.  The spelling must be exact on each one.
X.plot.seqids := "SL2.50ch01"    # Use "" for all
Y.plot.seqids := "Spenn-ch01"    # Use "" for all


# What should be the starting and ending plot position on the sequence ID when
# X.plot.seqids/Y.plot.seqids is just a SINGLE sequence ID?  Set start and end
# to 0 to cause the entire sequence ID to be plotted.  These values are in Mbp.
X.plot.start := 6.25
Y.plot.start := 6.5
X.plot.end := 8
Y.plot.end := 8.25


# Color, width, and inter-chromosome spacing of chromosome lines.  (Or whatever
# kind of sequence the sequence IDs represent).  Width is in arbitrary units.
# Spacing is in Mbp since axes are plotted in genome Mbp position.
X.chr.color := white
Y.chr.color := white
X.chr.width := 10
Y.chr.width := 10
X.chr.spacing := 5
Y.chr.spacing := 5


# Should a chromosome label be plotted for each chromosome or sequence ID?
PLOT.chr.label := TRUE    # Else FALSE


# If PLOT.chr.label is TRUE, chromosome label position, color, and size.
# Position is 0 for neutral, negative for inward, positive for outward.
# If PLOT.chr.label is FALSE, these are ignored but still must be present
# in this file.
X.chr.label.position := 2
Y.chr.label.position := 1
X.chr.label.color := white
Y.chr.label.color := white
X.chr.label.size := 3
Y.chr.label.size := 3


# If PLOT.chr.label is TRUE, the sequence ID can be edited to extract just the
# portion to be placed on the label, since the entire ID may be lengthy.  Define
# a regular expression to match a sequence ID, and a replacement expression to
# replace the matched text.  If you don't know what regular expressions and
# their replacement expressions look like, either get someone to help, or you
# simply specify for the RE the fixed text sequence you would like removed from
# the ID, and set RE.replace to "".  If RE is "", the sequence IDs are plotted
# as they are.  If PLOT.chr.label is FALSE, these are ignored but still must be
# present in this file.
X.chr.label.RE := "^SL2.50(ch[0-9]+)$"
X.chr.label.replace := "\1"
Y.chr.label.RE := "^Spenn-(ch[0-9]+)$"
Y.chr.label.replace := "\1"


# Axis label text, position, color, and size.  If text is "", no label is plotted.
# Position is 0 for neutral, negative for inward, positive for outward.  If the
# text is "", the related values are ignored but still must be present in this file.
X.axis.label.text := "S. lycopersicum"
Y.axis.label.text := "S.pennellii"
X.axis.label.position := 6
Y.axis.label.position := 4
X.axis.label.color := white
Y.axis.label.color := white
X.axis.label.size := 5
Y.axis.label.size := 5

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# End of file.
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