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 complete listing of the customization options for each chart.

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 = "Chromosome" — 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 = "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

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 = "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

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)

iplotMScanone (no 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=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 = "Chromosome" — 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

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 = "Chromosome" — 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

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

iplotCorr

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_yN