# A web interface for gene-set enrichment analyses

## Documentation for package ‘gCMAPWeb’ version 1.26.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

gCMAPWeb-package | A web-interface for gene-set enrichment analysis
addLinks | Adding links to columns of a data.frame
add_geneScores_to_df | CMAPResults data.frame with gene-level scores
body_first | Definition of html navigation bar elements
cmap-data | Example reference datasets
cmap1 | Example reference datasets
cmap2 | Example reference datasets
cmap3 | Example reference datasets
cmap4 | Example reference datasets
cmap5 | Example reference datasets
cmapAnalysis | Function controlling the gCMAP analysis workflow
cmapHeatmap | Function to create an annotated heatmap of gene scores
cmapRun | cmapRun
cmapRun-method | cmapRun
conversion_html | Identifier conversion html output
convert_gene_identifiers | Entrez mapper
create_figure_legend | This function generates the figure legend, with a separate dom identifier for each output panel
create_GeneIdentifierType | GeneIdentifierType creator
create_GeneSet | GeneSet creator
create_gene_report | This function compiles a gene-level report from a CMAPResults object.
create_gene_table_legend | This function reads an eSet object and returns the html code to display a legend for all columns that have more descriptive annotations in the varMetadata slot.
create_heatmap_legend | Legend for overview heatmap

create_legend

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.

create_overview_legend | Legend for overview density plot
create_overview_plot | Overview plot
create_profile_ExpressionSet | ExpressionSet creator
create_query_objects | Query object creator
create_SignedGeneSet | SignedGeneSet creator
create_tab | Create tab-delimited output
create_zip | Export gCMAPWeb report as zip archive
entrez_GeneSets | GeneSet Entrez mapper
exampleCMAP | Generate example NChannelSets
examplePost | Simulate POST request
gCMAPWeb | Start local gCMAPWeb instance
generate_report | gCMAPWeb reporting function
gene_density_chart_legend | Html code for the legend of pie the pie chart of the gene-level report
gene_density_profile_legend | Html code for the legend of the density charts of the gene-level reports from Profile queries
gene_pie_chart_legend | Html code for the legend of the pie chart of the gene-level report
hide_species_js | Javascript code to hide html elements
html_body_last | Html footer
html_header | Html header and bootstrap css stylesheet
html_table | Format data.frame as html table
identifier_radio_html | Html code for identifier type radio button selectors
index_message | Html code for text of the additional message on the index page (warning box)
index_quote | Html code for quote on the index page
index_subtitle | Html code for subtitle of the hero unit of the index.rhtml page
index_text | Html code for text of the hero unit of the index.rhtml page
index_title | Html code for title of the hero unit of the index.rhtml page
inputType_buttons | Html code for the query type selection buttons on the gCMAPWeb index page
load_cmaps | Loading reference datasets
parse_file_input | Uploaded file parser
parse_request | POST request parser
parse_textarea_input | Textarea parser
platform_radio_html | Html code for platform radio button selectors
process_score_input | Score parser
profile_input_example | Html code for generating an example query button on the profile submission page
read_config_file | Parser for gCMAPWeb configuration file
reference_radio_html | Html code for reference cmap radio button selectors
retrieve_annotation | Gene symbol and name lookup
signed_input_example | Html code for generating and example query button on the signed gene set submission page
single_input_example | Html code for generating and example query button on the single gene query submission page
species_radio_html | Html code for species radio button selectors
stripPrefix | Strip prefix from gene identifier names
unsigned_input_example | Html code for generating and example query button on the unsigned gene set submission page
validate_config_file | Validation of gCMAPWeb configuration file
validate_request | Html request validation