This function reads a CMAPResults object and returns the html code to display a legend for all columns that have more descriptive annotations in the varMetadata slot. A standard set of columns is selected for display in the legend through the 'keep' parameter. In addition, all columns with annotations in the labelDescription field of the varMetadata slot are included if the field content differs from the column name.

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Description

This function reads a CMAPResults object and returns the html code to display a legend for all columns that have more descriptive annotations in the varMetadata slot. A standard set of columns is selected for display in the legend through the 'keep' parameter. In addition, all columns with annotations in the labelDescription field of the varMetadata slot are included if the field content differs from the column name.

Usage

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create_legend(res, reference.name, keep = c("set", "trend", "FDR", "effect",
  "nSet", "Genes"), swap.colnames = getOption("swap.colnames", default =
  list(padj = "FDR", nFound = "Genes")))

Arguments

res

CMAPResults object

reference.name

character, ame of the reference database used

keep

character, a vector with column names that are always included in the legend

swap.colnames

list, containing alternative names for CMAPResults columns.

Value

character string with the html code element required to insert the legend into the html report

Author(s)

Thomas Sandmann

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