multtrait: Plot 1-D scan of LOD and/or means

In byandell/qtlview: Visualization of QTL Scans for Multiple Traits

Description

Profiles of one or more phenotypes using raw data or pre-computed profiles. If only one phenotype, in addition profile the means by genotype.

Usage

multtrait(traitnames = NULL, cross.name, cross = get(cross.name),
  category, filename = NULL, chr="", main = "",
  summary.plot = c("total", "chr","none","phenotype"),
  threshold.level=0.05, threshold.lod,
  cluster = TRUE, support.lod = 1.5,
  n.clust,
  heatmap = FALSE,
  scan.type = c("LOD","LPD","BF","RAW","MOM","PAT"),
  sex = c("both","male","female"),
  ylab = c("symbol","a_gene_id","symbol.a_gene_id","none","on"),
  ...)  
## S3 method for class 'multtrait'
plot(x, heatmap = TRUE, rescale = TRUE, use.cM = FALSE,
  summary.plot, ...)
## S3 method for class 'multtrait'
summary(object, ...)
## S3 method for class 'multtrait'
print(x, ...)

Details

multtrait is intended as the Intranet interface.

See Also

myplot

Examples

multtrait.plot(cross.name="B6BTBR07",
  category="rbm", ## Later this will allow for tissues, modules.
  traitnames=mytrait(c("il.18","mpo")),
  chr=c(1:19,"X"),
  col.scheme=c("redblue", "cm", "gray", "heat", "terrain",
        "topo"),
  threshold.level=0.05,    ## Drop traits that have max below threshold.
  max.names=100,           ## Include names if number of traits < max.names.
  max.lod = 20)            ## Truncate lod at max.lod for color scheme.

byandell/qtlview documentation built on May 13, 2019, 9:53 a.m.