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.)
iboxplotwidth = 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
idotplotheight = 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
iheatmapheight = 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
ipleiotropyheight = 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)
iplotheight = 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
iplotCurvesheight = 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
iplotMapwidth = 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
iplotRFheight = 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)
iplotScantwoheight = 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
itriplotwidth = 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
scat2scatheight = 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)