There are a number of ways in which one may wish to customize the interactive graphs produced by R/qtlcharts, such as different colors or axis labels. Our main approach to allow such customization is through a function argument, chartOpts.

Use of these options is described in the R/qtlcharts User Guide.

The following is a listing of the customization options for each chart. You can also use the chart option caption to provide a caption for the chart. (The caption option is mostly intended for stand-alone html files.)

iboxplot

width = 1000 — width of image in pixels

height = 900 — total height of image in pixels

margin = list(left=60, top=20, right=60, bottom=40) — margins in pixels (left, top, right, bottom)

ylab = "Response" — y-axis label

xlab = "Individuals" — x-axis label

rectcolor = "#E6E6E6" — color of background rectangle

qucolors = NULL — vector of colors for the quantile curves

histcolors = c("#0074D9", "#FF4136", "#3D9970", "MediumVioletRed", "black") — vector of colors for selected histograms

idotplot

height = 550 — height of chart in pixels

width = 400 — width of chart in pixels

title = "" — title for chart

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

xlab = "group" — x-axis label

ylab = "response" — y-axis label

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

jitter = "beeswarm" — method for jittering points (beeswarm|random|none)

ylim = NULL — y-axis limits

yticks = NULL — vector of tick positions on y-axis

nyticks = 5 — no. ticks on y-axis

rectcolor = "#E6E6E6" — color of background rectangle

pointcolor = NULL — color for points

pointsize = 3 — size of points in pixels

pointstroke = "black" — color of outer circle for points

yNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values (handle=T/F, force=T/F, width, gap)

xcategories = NULL — group categories

xcatlabels = NULL — labels for group categories

horizontal = false — If true, have genotypes on vertical axis and phenotype on horizontal axis

iheatmap

height = 800 — total height of chart

width = 800 — total width of chart

htop = height/2 — height of top charts in pixels

wleft = width/2 — width of left charts in pixels

margin = list(left=60, top=40, right=40, bottom=40, inner=0) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

rectcolor = "#E6E6E6" — color of background rectangle

nullcolor = "#E6E6E6" — color of pixels with null values

linecolor = "slateblue" — line color

linewidth = 2 — line width

xlim = NULL — x-axis limits

ylim = NULL — y-axis limits

nxticks = 5 — no. ticks on x-axis

xticks = NULL — vector of tick positions on x-axis

nyticks = 5 — no. ticks on y-axis

yticks = NULL — vector of tick positions on y-axis

nzticks = 5 — no. ticks on z-axis

zticks = NULL — vector of tick positions on z-axis

title = "" — title for chart

xlab = "X" — x-axis label

ylab = "Y" — y-axis label

zlab = "Z" — z-axis label

zthresh = NULL — lower threshold for plotting in heat map: only values with |z| > zthresh are shown

zlim = c(-d3panels.max(z), 0, d3panels.max(z)) — z-axis limits

colors = c("slateblue", "white", "crimson") — heat map colors (same length as zlim)

flip_vert_slice = false — if true, flip the y- and z- axes in the vertical slice

ipleiotropy

height = 450 — height of image in pixels

width = 900 — width of image in pixels

wleft = width*0.5 — width of left panel in pixels (ignored if LOD scores not provided)

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

lod_axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel) in LOD curve panel

lod_titlepos = 20 — position of title for LOD curve panel, in pixels

rectcolor = "#E6E6E6" — color of background rectangle

lod_ylim = NULL — y-axis limits in LOD curve panel

lod_nyticks = 5 — number of ticks in y-axis in LOD curve panel

lod_yticks = NULL — vector of tick positions for y-axis in LOD curve panel

linecolor = c("darkslateblue", "orchid") — line colors for LOD curves

linewidth = 2 — line width for LOD curves

lod_title = "" — title of LOD curve panel

lod_xlab = "Chromosome" — x-axis label for LOD curve panel

lod_ylab = "LOD score" — y-axis label for LOD curve panel

lod_rotate_ylab = NULL — indicates whether to rotate the y-axis label 90 degrees, in LOD curve panel

pointcolor = NULL — vector of point colors for phenotype scatter plot (non-recombinants first, then all of the recombinants)

pointstroke = "black" — color of outer circle for points, in scatterplot

pointsize = 3 — point size in phe-by-gen paenl

scat_ylim = NULL — y-axis limits in scatterplot

scat_nyticks = 5 — number of ticks in y-axis in scatterplot

scat_yticks = NULL — vector of tick positions for y-axis in scatterplot

scat_xlab = NULL — x-axis label in scatterplot

scat_ylab = NULL — y-axis label in scatterplot

scat_rotate_ylab = NULL — indicates whether to rotate the y-axis label 90 degrees, in scatterplot

scat_axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel) in LOD curve panel

scat_titlepos = 20 — position of title for scatterplot, in pixels

scat_title = "" — title of scatterplot panel

slider_height = 80 — height of slider

slider_color = "#E6E6E6" — color of slider bar

button_color = "#E6E6E6" — color of rectangular part of buttons

ticks_at_markers = true — if true, put tick marks at the marker positions (above the slider)

iplot

height = 500 — height of chart in pixels

width = 800 — width of chart in pixels

title = "" — title for chart

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

xlab = "X" — x-axis label

ylab = "Y" — y-axis label

xlim = NULL — x-axis limits

xticks = NULL — vector of tick positions on x-axis

nxticks = 5 — no. ticks on x-axis

ylim = NULL — y-axis limits

yticks = NULL — vector of tick positions on y-axis

nyticks = 5 — no. ticks on y-axis

rectcolor = "#E6E6E6" — color of background rectangle

pointcolor = NULL — colors for points

pointsize = 3 — size of points in pixels

pointstroke = "black" — color of outer circle for points

rotate_ylab = NULL — whether to rotate the y-axis label

xNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values (handle=T/F, force=T/F, width, gap)

yNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values (handle=T/F, force=T/F, width, gap)

iplotCorr (with scatterplot)

height = 560 — height of each panel in pixels

width = 1050 — total width of panels

margin = list(left=70, top=40, right=5, bottom=70, inner=5) — margins in pixels (left, top, right, bottom, inner)

corcolors = c("darkslateblue", "white", "crimson") — heat map colors (same length as zlim)

zlim = c(-1, 0, 1) — z-axis limits

rectcolor = "#E6E6E6" — color of background rectangle

cortitle = "" — title for heatmap panel

scattitle = "" — title for scatterplot panel

scatcolors = NULL — vector of point colors for scatterplot

pointsize = 3 — size of points in scatterplot

iplotCorr (no scatterplot)

height = 560 — height of each panel in pixels

width = 1050 — total width of panels

margin = list(left=70, top=40, right=5, bottom=70, inner=5) — margins in pixels (left, top, right, bottom, inner)

corcolors = c("darkslateblue", "white", "crimson") — heat map colors (same length as zlim)

zlim = c(-1, 0, 1) — z-axis limits

rectcolor = "#E6E6E6" — color of background rectangle

cortitle = "" — title for heatmap panel

iplotCurves

height = 1000 — total height of chart in pixels

width = 1000 — total width of chart in pixels

htop = height/2 — height of curves chart in pixels

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

rectcolor = "#E6E6E6" — color of background rectangle

pointcolor = NULL — vector of colors for points in scatterplots

pointstroke = "black" — color of line outline for points in scatterplots

pointsize = 3 — size of points in scatterplots

pointcolorhilit = NULL — vector of colors for points in scatterplots, when highlighted

pointsizehilit = 6 — size of points in scatterplot, when highlighted

linecolor = NULL — vector of colors of curves

linecolorhilit = NULL — vector of colors of curves, when highlighted

linewidth = 2 — line width of curves

linewidthhilit = 2 — line widths of curves, when highlighted

curves_xlim = NULL — x-axis limits in curve plot

curves_ylim = NULL — y-axis limits in curve plot

curves_nxticks = 5 — no. ticks on x-axis in curve plot

curves_xticks = NULL — vector of tick positions on x-axis in curve plot

curves_nyticks = 5 — no. ticks on y-axis in curve plot

curves_yticks = NULL — vector of tick positions on y-axis in curve plot

curves_title = "" — title for curve plot

curves_xlab = "X" — x-axis label for curve plot

curves_ylab = "Y" — y-axis label for curve plot

scat1_xlim = NULL — x-axis limits in first scatterplot

scat1_ylim = NULL — y-axis limits in first scatterplot

scat1_xNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values for x variable in first scatterplot (handle=T/F, force=T/F, width, gap)

scat1_yNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values for x variable in first scatterplot (handle=T/F, force=T/F, width, gap)

scat1_nxticks = 5 — no. ticks on x-axis in first scatterplot

scat1_xticks = NULL — vector of tick positions on x-axis in first scatterplot

scat1_nyticks = 5 — no. ticks on y-axis in first scatterplot

scat1_yticks = NULL — vector of tick positions on y-axis in first scatterplot

scat1_title = "" — title for first scatterplot

scat1_xlab = "X" — x-axis label for first scatterplot

scat1_ylab = "Y" — y-axis label for first scatterplot

scat2_xlim = NULL — x-axis limits in second scatterplot

scat2_ylim = NULL — y-axis limits in second scatterplot

scat2_xNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values for x variable in second scatterplot (handle=T/F, force=T/F, width, gap)

scat2_yNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values for x variable in second scatterplot (handle=T/F, force=T/F, width, gap)

scat2_nxticks = 5 — no. ticks on x-axis in second scatterplot

scat2_xticks = NULL — vector of tick positions on x-axis in second scatterplot

scat2_nyticks = 5 — no. ticks on y-axis in second scatterplot

scat2_yticks = NULL — vector of tick positions on y-axis in second scatterplot

scat2_title = "" — title for second scatterplot

scat2_xlab = "X" — x-axis label for second scatterplot

scat2_ylab = "Y" — y-axis label for second scatterplot

iplotMScanone (no effects)

height = 700 — height of chart in pixels

width = 1000 — width of chart in pixels

title = "" — title for chart

wleft = width*0.65 — width of left panels in pixels

htop = height/2 — height of top panels in pixels

margin = list(left=60, top=40, right=40, bottom=40, inner=0) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

chrGap = 6 — gap between chromosomes in pixels

rectcolor = "#E6E6E6" — color of lighter background rectangle

altrectcolor = "#C8C8C8" — color of darker background rectangle

nullcolor = "#E6E6E6" — color for pixels with null values

chrlinecolor = "" — color of lines between chromosomes (if "", leave off)

chrlinewidth = 2 — width of lines between chromosomes

colors = c("slateblue", "white", "crimson") — heat map colors

zlim = NULL — z-axis limits

zthresh = NULL — lower z-axis threshold for display in heat map

xlab = NULL — x-axis label for LOD heatmap)

ylab = "" — y-axis label for LOD heatmap (also used as x-axis label on effect plot)

zlab = "LOD score" — z-axis label for LOD heatmap (really just used as y-axis label in the two slices)

linecolor = "darkslateblue" — color of LOD curves

linewidth = 2 — width of LOD curves

pointsize = 0 — size of points in vertical slice (default = 0 corresponds plotting curves rather than points)

pointcolor = "slateblue" — color of points in vertical slice

pointcolorhilit = "crimson" — color of highlighted point in vertical slice

pointstroke = "black" — color of outer circle for points in vertical slice

nxticks = 5 — no. ticks in x-axis on right-hand panel, if quantitative scale

xticks = NULL — tick positions in x-axis on right-hand panel, if quantitative scale

iplotMScanone (with effects)

height = 700 — height of chart in pixels

width = 1000 — width of chart in pixels

wleft = width*0.65 — width of left panels in pixels

htop = height/2 — height of top panels in pixels

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

title = "" — title for chart

chrGap = 6 — gap between chromosomes in pixels

rectcolor = "#e6e6e6" — color of background rectangle

altrectcolor = "#c8c8c8" — color of alternate background rectangle

nullcolor = "#e6e6e6" — color for pixels with null values

chrlinecolor = "" — color of lines between chromosomes (if "", leave off)

chrlinewidth = 2 — width of lines between chromosomes

colors = c("slateblue", "white", "crimson") — heat map colors

zlim = NULL — z-axis limits

zthresh = NULL — lower z-axis threshold for display in heat map

xlab = NULL — x-axis label for LOD heatmap (also used in lower panel)

ylab = "" — y-axis label for LOD heatmap (also used as x-axis label on effect plot)

zlab = "LOD score" — z-axis label for LOD heatmap (really the y-axis label in the lower panel)

eff_ylim = NULL — y-axis limits for effect plot (right panel)

eff_ylab = "" — y-axis label for effect plot (right panel)

linecolor = "darkslateblue" — line color for LOD curves (lower panel)

linewidth = 2 — line width for LOD curves (lower panel)

eff_linecolor = NULL — line color for effect plot (right panel)

eff_linewidth = 2 — width of line for effect plot (right panel)

eff_pointcolor = NULL — point color for effect plot (right panel)

eff_pointsize = 0 — point size for effect plot (right panel); 0 means no points

eff_pointstroke = "black" — stroke color for points in effect plot (right panel)

nxticks = 5 — no. ticks in x-axis for effect plot (right panel), if quantitative scale

xticks = NULL — tick positions in x-axis for effect plot (right panel), if quantitative scale

lod_labels = NULL — labels on the LOD score columns

iplotMap

width = 1000 — width of chart in pixels

height = 600 — height of chart in pixels

margin = list(left=60, top=40, right=100, bottom=40, inner=10) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

ylim = NULL — y-axis limits

nyticks = 5 — no. ticks on y-axis

yticks = NULL — vector of tick positions on y-axis

xlineOpts = list(color="#cdcdcd", width=5) — color and width of vertical lines

tickwidth = 10 — width of tick marks at markers, in pixels

rectcolor = "#E6E6E6" — color of background rectangle

linecolor = "slateblue" — color of lines

linecolorhilit = "Orchid" — color of lines, when highlighted

linewidth = 3 — width of lines

title = "" — title for chart

xlab = "Chromosome" — x-axis label

ylab = "Position (cM)" — y-axis label

shiftStart = false — if true, shift the start of chromosomes to 0

horizontal = false — if true, have chromosomes on vertical axis and positions horizontally

iplotRF

height = 800 — total height of chart in pixels

width = 1000 — total width of chart in pixels

hbot = 300 — height (in pixels) of each of the lower panels with LOD scores

margin = list(left=60, top=40, right=40, bottom=60) — margins in pixels (left, top, right, bottom)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — axis positions in heatmap

titlepos = 20 — position of chart title in pixels

chrGap = 2 — gaps between chr in heat map

chrlinecolor = "" — color of lines between chromosomes (if "", leave off)

chrlinewidth = 2 — width of lines between chromosomes

oneAtTop = false — if true, put chromosome 1 at the top rather than bottom

colors = c("crimson", "white", "slateblue") — vector of three colors for the color scale (negative - zero - positive)

nullcolor = "#e6e6e6" — color for empty cells

zlim = NULL — z-axis limits (if null take from data, symmetric about 0)

zthresh = NULL — z threshold; if |z| < zthresh, not shown

hilitCellcolor = "black" — color of box around highlighted cell

cellPad = NULL — padding of cells (if null, we take cell width * 0.1)

fontsize = NULL — font size in crosstab

rectcolor = "#e6e6e6" — background rectangle color (and color of cells in crosstab)

altrectcolor = "#c8c8c8" — alternate rectangle color in lower panels with LOD and rf

hilitcolor = "#e9cfec" — color of rectangle in heatmap when highlighted

boxcolor = "black" — color of outer box of panels

boxwidth = 2 — width of outer box in pixels

pointsize = 2 — point size in lower panels with LOD and rf

pointcolor = "slateblue" — point color in lower panels with LOD and rf

pointstroke = "black" — stroke color for points in lower panels with LOD and rf

lodlim = c(0, 12) — range of LOD values to display; omit below 1st, truncate above 2nd

nyticks = 5 — no. ticks on y-axis in LOD curve panels

yticks = NULL — vector of tick positions on y-axis in LOD curve panels

tipclass = "tooltip" — class name for tool tips

iplotScanone (no effects)

height = 450 — height of image in pixels

width = 900 — width of image in pixels

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

ylim = NULL — y-axis limits

nyticks = 5 — number of ticks in y-axis

yticks = NULL — vector of tick positions for y-axis

chrGap = 6 — gap between chromosomes in pixels

rectcolor = "#E6E6E6" — color of background rectangle

altrectcolor = "#C8C8C8" — color of alternate background rectangle

linecolor = "darkslateblue" — line color for LOD curves

linewidth = 2 — line width for LOD curves

pointcolor = "#E9CFEC" — color for points at markers

pointsize = 0 — size of points at markers (default = 0 corresponding to no visible points at markers)

pointstroke = "black" — color of outer circle for points at markers

title = "" — title of chart

xlab = NULL — x-axis label

ylab = "LOD score" — y-axis label

rotate_ylab = NULL — indicates whether to rotate the y-axis label 90 degrees

iplotScanone (pxgtype='ci')

height = 530 — height of image in pixels

width = 1200 — width of image in pixels

wleft = width*0.7 — width of left panel in pixels

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

lod_axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel) in LOD curve panel

lod_titlepos = 20 — position of title for LOD curve panel, in pixels

chrGap = 6 — gap between chromosomes

rectcolor = "#E6E6E6" — color of lighter background rectangle

altrectcolor = "#C8C8C8" — color of darker background rectangle

lod_ylim = NULL — y-axis limits in LOD curve panel

lod_nyticks = 5 — number of ticks in y-axis in LOD curve panel

lod_yticks = NULL — vector of tick positions for y-axis in LOD curve panel

lod_linecolor = "darkslateblue" — line color for LOD curves

lod_linewidth = 2 — line width for LOD curves

lod_pointcolor = "#E9CFEC" — color for points at markers in LOD curve panel

lod_pointsize = 0 — size of points at markers (default = 0 corresponding to no visible points at markers)

lod_pointstroke = "black" — color of outer circle for points at markers in LOD curve panel

lod_title = "" — title of LOD curve panel

lod_xlab = NULL — x-axis label for LOD curve panel

lod_ylab = "LOD score" — y-axis label for LOD curve panel

lod_rotate_ylab = NULL — indicates whether to rotate the y-axis label 90 degrees, in LOD curve panel

eff_ylim = NULL — y-axis limits in effect plot panel

eff_nyticks = 5 — number of ticks in y-axis in effect plot panel

eff_yticks = NULL — vector of tick positions for y-axis in effect plot panel

eff_linecolor = "slateblue" — line color in effect plot panel

eff_linewidth = "3" — line width in effect plot panel

eff_xlab = "Genotype" — x-axis label in effect plot panel

eff_ylab = "Phenotype" — y-axis label in effect plot panel

eff_rotate_ylab = NULL — indicates whether to rotate the y-axis label 90 degrees, in effect plot panel

eff_segwidth = NULL — width of line segments in effect plot panel, in pixels

eff_axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel) in effect plot panel

eff_titlepos = 20 — position of title for effect plot panel, in pixels

iplotScanone (pxgtype='raw')

height = 450 — height of image in pixels

width = 1200 — width of image in pixels

wleft = width*0.7 — width of left panel in pixels

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

lod_axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel) in LOD curve panel

lod_titlepos = 20 — position of title for LOD curve panel, in pixels

chrGap = 6 — gap between chromosomes

rectcolor = "#E6E6E6" — color of background rectangle

altrectcolor = "#C8C8C8" — color of alternate background rectangle

lod_ylim = NULL — y-axis limits in LOD curve panel

lod_nyticks = 5 — number of ticks in y-axis in LOD curve panel

lod_yticks = NULL — vector of tick positions for y-axis in LOD curve panel

lod_linecolor = "darkslateblue" — line color for LOD curves

lod_linewidth = 2 — line width for LOD curves

lod_pointcolor = "#E9CFEC" — color for points at markers in LOD curve panel

lod_pointsize = 0 — size of points at markers (default = 0 corresponding to no visible points at markers)

lod_pointstroke = "black" — color of outer circle for points at markers in LOD curve panel

lod_title = "" — title of LOD curve panel

lod_xlab = NULL — x-axis label for LOD curve panel

lod_ylab = "LOD score" — y-axis label for LOD curve panel

lod_rotate_ylab = NULL — indicates whether to rotate the y-axis label 90 degrees, in LOD curve panel

eff_pointcolor = "slateblue" — point color in phe-by-gen panel

eff_pointcolorhilit = "Orchid" — point color, when highlighted, in phe-by-gen panel

eff_pointstroke = "black" — color of outer circle for points, in phe-by-gen panel

eff_pointsize = 3 — point size in phe-by-gen paenl

eff_ylim = NULL — y-axis limits in phe-by-gen panel

eff_nyticks = 5 — number of ticks in y-axis in phe-by-gen panel

eff_yticks = NULL — vector of tick positions for y-axis in phe-by-gen panel

eff_xlab = "Genotype" — x-axis label in phe-by-gen panel

eff_ylab = "Phenotype" — y-axis label in phe-by-gen panel

eff_rotate_ylab = NULL — indicates whether to rotate the y-axis label 90 degrees, in phe-by-gen panel

xjitter = NULL — amount of horizontal jittering in phe-by-gen panel

eff_axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel) in LOD curve panel

eff_titlepos = 20 — position of title for phe-by-gen panel, in pixels

eff_yNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values in phe-by-gen panel (handle=T/F, force=T/F, width, gap)

iplotScantwo

height = 1200 — total height of chart in pixels

width = 1100 — total width of chart in pixels

chrGap = 2 — gaps between chr in heat map

wright = width/2 — width (in pixels) of right panels

hbot = height/5 — height (in pixels) of each of the lower panels

margin = list(left=60, top=50, right=10, bottom=40, inner=5) — margins in each panel

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — axis positions in heatmap

titlepos = 20 — position of chart title in pixels

rectcolor = "#e6e6e6" — color for background rectangle

altrectcolor = "#c8c8c8" — alternate rectangle in lower panels

chrlinecolor = "" — color of lines between chromosomes (if "", leave off)

chrlinewidth = 2 — width of lines between chromosomes

nullcolor = "#e6e6e6" — color of null pixels in heat map

boxcolor = "black" — color of box around each panel

boxwidth = 2 — width of box around each panel

linecolor = "slateblue" — line color in lower panels

linewidth = 2 — line width in lower panels

pointsize = 2 — point size in right panels

pointstroke = "black" — color of outer circle in right panels

cicolors = NULL — colors for CIs in QTL effect plot; also used for points in phe x gen plot

segwidth = 0.4 — segment width in CI chart as proportion of distance between categories

segstrokewidth = 3 — stroke width for segments in CI chart

color = "slateblue" — color for heat map

oneAtTop = false — whether to put chr 1 at top of heatmap

zthresh = 0 — LOD values below this threshold aren’t shown (on LOD_full scale)

ylab_eff = "Phenotype" — y-axis label in dot and ci charts

xlab_lod = "Chromosome" — x-axis label in lod charts

ylab_lod = "LOD score" — y-axis label in lod charts

nyticks_lod = 5 — no. ticks on y-axis in LOD curve panels

yticks_lod = NULL — vector of tick positions on y-axis in LOD curve panels

nyticks_ci = 5 — no. ticks on y-axis in CI panel

yticks_ci = NULL — vector of tick positions on y-axis in CI panel

nyticks_pxg = 5 — no. ticks on y-axis in dot chart of phenotype x genotype

yticks_pxg = NULL — vector of tick positions on y-axis in dot chart of phenotype x genotype

itriplot

width = 600 — overall width of chart in pixels

height = 520 — overall height of chart in pixels

margin = list(left=60, top=40, right=60, bottom=10) — margins in pixels (left, top, right, bottom)

labelpos = 10 — pixels between vertex and vertex label (horizontally)

titlepos = 20 — position of chart title in pixels

title = "" — chart title

labels = c("(1,0,0)", "(0,1,0)", "(0,0,1)") — labels on the corners

rectcolor = "#e6e6e6" — color of background rectangle

boxcolor = "black" — color of outer rectangle box

boxwidth = 2 — width of outer box in pixels

pointcolor = NULL — fill color of points

pointstroke = "black" — color of points’ outer circle

pointsize = 3 — size of points in pixels

gridlines = 0 — number of grid lines

gridcolor = "white" — color of grid lines

gridwidth = 1 — width of grid lines in pixels

tipclass = "tooltip" — class name for tool tips

scat2scat

height = 500 — height of chart in pixels

width = 800 — width of chart in pixels

title1 = "" — title for left panel

margin = list(left=60, top=40, right=40, bottom=40, inner=5) — margins in pixels (left, top, right, bottom, inner)

axispos = list(xtitle=25, ytitle=30, xlabel=5, ylabel=5) — position of axis labels in pixels (xtitle, ytitle, xlabel, ylabel)

titlepos = 20 — position of chart title in pixels

xlab1 = "X" — x-axis label for left panel

ylab1 = "Y" — y-axis label for left panel

xlab2 = "X" — x-axis label for right panel (can be a vector, with separate values for each dataset in scat2data)

ylab2 = "Y" — y-axis label for right panel (can be a vector, with separate values for each dataset in scat2data)

xlim1 = NULL — x-axis limits for left panel

xticks1 = NULL — vector of tick positions on x-axis for left panel

nxticks1 = 5 — no. ticks on x-axis for left panel

ylim1 = NULL — y-axis limits for left panel

yticks1 = NULL — vector of tick positions on y-axis for left panel

nyticks1 = 5 — no. ticks on y-axis for left panel

xlim2 = NULL — x-axis limits for right panel

xticks2 = NULL — vector of tick positions on x-axis for right panel

nxticks2 = 5 — no. ticks on x-axis for right panel

ylim2 = NULL — y-axis limits for right panel

yticks2 = NULL — vector of tick positions on y-axis for right panel

nyticks2 = 5 — no. ticks on y-axis for right panel

rectcolor = "#E6E6E6" — color of background rectangle

pointcolor1 = NULL — colors for points for left panel

pointsize1 = 3 — size of points in pixels for left panel

pointstroke1 = "black" — color of outer circle for points for left panel

pointcolor2 = NULL — colors for points for right panel

pointsize2 = 3 — size of points in pixels for right panel

pointstroke2 = "black" — color of outer circle for points for right panel

rotate_ylab1 = NULL — whether to rotate the y-axis label in left panel

rotate_ylab2 = NULL — whether to rotate the y-axis label in right panel

xNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values (handle=T/F, force=T/F, width, gap)

yNA = list(handle=true, force=false, width=15, gap=10) — treatment of missing values (handle=T/F, force=T/F, width, gap)