#' @describeIn CTDdata Generates a basic plot showing the number of terms
#' that can be used to query CTDbase.
#' @param x Object of class \code{CTDdata}.
#' @param y NOT USED
#' @param index_name Name of the plot to be draw. See \code{\link{CTDdata}}'s
#' detail section for more information (\code{?`CTDdata-class`}).
#' representation.
#' @param representation Can take values \code{"heatmap"} or \code{"network"}.
#' @export
setMethod(
f = "plot",
signature = "CTDdata",
definition = function( x, y, index_name = "base", representation = "heatmap", ... ) {
index_name <- base::tolower( index_name )
if( x@type == "VOID" ) {
warning( "No data was provided" )
return(invisible())
}
if( index_name == "base" ) {
in_plot_base( x )
} else {
if( x@type == "GENE" ) { ## BLUE
if( index_name == "disease" ) {
if( representation == "heatmap" ) {
int_plot_gene_disease_heatmap( x, ... )
} else {
stop( "No network representation for 'disease association'." )
}
} else if( index_name == "chemical interactions" ) {
if( representation == "heatmap" ) {
int_plot_gene_chemical_heatmap( x, ... )
} else {
stop( "No network representation for 'disease association'." )
}
} else if( index_name == "gene-gene interactions" ) {
if( representation == "heatmap" ) {
warning( "Are you sure you dont what to use 'network' representation?" )
int_plot_gene_gene_heatmap( x, ... )
} else if ( representation == "network" ) {
int_plot_gene_gene_network( x, ... )
} else {
stop( "Only available 'heatmap' and 'network' representations." )
}
} else if( index_name == "kegg pathways" ) {
if( representation == "heatmap" ) {
stop( "No heatmap representation for 'kegg pathways'." )
} else {
int_plot_gene_kegg_network( x, ... )
}
} else if( index_name == "go terms" ) {
if( representation == "heatmap" ) {
stop( "No heatmap representation for 'go terms'." )
} else {
int_plot_gene_go_network( x, ... )
}
} else {
stop( "Invalid provided 'index_name' for 'GENE' query. ")
}
} else if( x@type == "CHEMICAL" ) { ## GREEN
if( index_name == "gene interactions" ) {
if( representation == "heatmap" ) {
int_plot_chem_gene_heatmap( x, ... )
} else {
int_plot_chem_gene_network( x, ... )
}
} else if( index_name == "disease" ) {
if( representation == "heatmap" ) {
int_plot_chem_disease_heatmap( x, ... )
} else {
stop( "No network representation for 'disease association'." )
}
} else if( index_name == "kegg pathways" ) {
if( representation == "heatmap" ) {
int_plot_chem_kegg_heatmap( x, ... )
} else {
stop( "No network representation for 'kegg pathways'." )
}
} else if( index_name == "go terms" ) {
if( representation == "heatmap" ) {
stop( "No heatmap representation for 'go terms'." )
} else {
int_plot_chem_go_heatmap( x, ... )
}
} else {
stop( "Invalid provided 'index_name' for 'CHEMICAL' query. ")
}
} else if( x@type == "DISEASE" ) {
if( index_name == "gene interactions" ) {
if( representation == "heatmap" ) {
int_plot_dise_gene_heatmap( x, ... )
} else {
stop( "No network representation for 'gene association'." )
}
} else if( index_name == "chemical interactions" ) {
if( representation == "heatmap" ) {
int_plot_disease_chemical_heatmap( x, ... )
} else {
stop( "No network representation for 'chemical association'." )
}
} else if( index_name == "kegg pathways" ) {
if( representation == "network" ) {
int_plot_dise_kegg_network( x, ... )
} else {
stop( "No heatmap representation for 'chemical association'." )
}
} else {
stop( "Invalid provided 'index_name' for 'DISEASE' query. ")
}
}
}
}
)
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