plotCheckerboard: plotCheckerboard

Description Usage Arguments Value Examples

Description

This plots checkerboard-style heatmaps of mean phenotype values in the diallel.

Usage

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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, ...)

Arguments

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

Value

Returns checkerboard plot

Examples

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mauriziopaul/PLMcctools documentation built on May 20, 2019, 5:43 p.m.