create_legend

character, ame of the reference database used

reference.name

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

keep

list, containing alternative names for CMAPResults columns.

swap.colnames


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.


The gCMAPWeb R package provides a graphical user interface
for the gCMAP package. gCMAPWeb uses the Rook package and can
be used either on a local machine, leveraging R's internal web
server, or run on a dedicated rApache web server installation.
gCMAPWeb allows users to search their own data sources and
instructions to generate reference datasets from public
repositories are included with the package. The package
supports three common types of analyses, specifically queries
with 1. one or two sets of query gene identifiers, whose
members are expected to show changes in gene expression in a
consistent direction. For example, an up-regulated gene set
might contain genes activated by a transcription factor, a
down-regulated geneset targets repressed by the same factor. 2.
a single set of query gene identifiers, whose members are
expected to show divergent differential expression
(non-directional query). For example, members of a particular
signaling pathway, some of which may be up- some down-regulated
in response to a stimulus. 3. a query with the complete results
of a differential expression profiling experiment. For example,
gene identifiers and z-scores from a previous perturbation
experiment. gCMAPWeb accepts three types of identifiers:
EntreIds, gene Symbols and microarray probe ids and can be
configured to work with any species supported by Bioconductor.
For each query submission, significantly similar reference
datasets will be identified and reported in graphical and
tabular form.

Thomas Sandmann

gCMAPWeb

A web interface for gene-set enrichment analyses

create_legend function

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.

Description

Usage

Arguments

Value