Description Usage Arguments Value Examples
This plots checkerboard-style heatmaps of mean phenotype values in the diallel.
1 2 3 4 5 6 7 8 9 10 11 | plotCheckerboard(summary.dat = NULL, phen = NULL,
aggregate.col = "Strain", fun = "mean", founder.ids = LETTERS[1:8],
main = "", xlab = "", founder.names = c("AJ", "B6", "129", "NOD", "NZO",
"CAST", "PWK", "WSB"), founder.letters = LETTERS[1:8],
founder.colors = c("#F0F000", "#808080", "#F08080", "#1010F0", "#00A0F0",
"#00A000", "#F00000", "#9000E0"), match.by = c("founder.letters",
"founder.names")[1], scale.palette = colorRampPalette(c("white", "black"))(n
= 1000), scale.range = range(summary.dat, na.rm = TRUE),
plot.palette = scale.palette, scale.tick = FALSE, which.tick = 5,
noscale = c(FALSE, TRUE)[1], scale.las = 1, axis.srt = 45,
axis.y.adj = 0.1, scale.cex = 1, scale.gradient.cex = 1, ...)
|
summary.dat |
summary data frame, summarized by strain-pair |
phen |
phenotype column name |
aggregate.col |
data frame column to aggregate by |
fun |
usually supplied as "mean", but could also be "sd" or some similar function of interest |
founder.ids |
usually letters A through ... |
founder.names |
descriptive names of founders, for axis labels |
founder.colors |
colors for founder lines, for axis plotting |
match.by |
choose founder.letters or founder.names, based on what is in input data frame |
scale.palette |
specify the palette to be used for color scale in the heatmap |
scale.range |
define the range of the data |
plot.palette |
specify the palette for the scale to be plotted, which may differ from the range of the palette of the plot |
scale.tick |
specify whether to highlight a mark on the axis with an additional tick |
which.tick |
specify which axis tick to highlight |
noscale |
boolean specifying whether to hide the scale |
scale.las |
specify the side of the scale axis using las |
axis.srt |
specify the angle to tilt the scale axis labels |
axis.y.adj |
specify a vertical adjustment for the scale axis labels |
scale.cex |
specify how big the scale text is using standard cex adjustments |
... |
additional arguments |
Returns checkerboard plot
1 | # Not Run
|
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