Description Usage Arguments Examples
This function produces a probability heatmap plot, ordered by the phenotype. This gives an idea of what the regression procedure is actually being handed as inputs.
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marker |
A marker that is contained in the genome cache. In general this should be a marker of interest, such as one beneath a putative QTL peak. |
p.value |
DEFAULT: NULL. Includes the observed p-value in the plot title. |
genomecache |
The path to the genome cache that contains founder haplotype information. |
model |
DEFAULT: "additive". If "additive", dosages are plotted. If "full", probabilities are plotted. |
phenotype |
The name of the phenotype column in the data set. |
phenotype.data |
A data.frame object that contains the phenotype information. Should also have a column that matches genomes in the genome cache. |
merge.by |
DEFAULT: "SUBJECT.NAME". Specifies the columns to merge phenotype and haplotype data. |
founder.labels |
DEFAULT: "NULL". If NULL, will default to the labels in the genome cache. |
founder.cex |
DEFAULT: 1. Defines the text size of the founder labels. |
include.ramp |
DEFAULT: TRUE. If TRUE, spectrum ramp for dosages or probabilities is included. |
include.marker |
DEFAULT: TRUE. If TRUE, the marker name is included in the title. |
alternative.phenotype.label |
DEFAULT: NULL. Allows for an alternative label for the phenotype. |
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