:- lib(col_faint/3). exp_gene_family_string_graph_defaults( Defs ) :- Defs = [ exp_ev_log(true), faint_factor(1.2), include_non_significant(true), include_non_present(false), % node_colours(clrs(red,green,yellow,khaki4,grey)), node_colours(clrs(tomato,steelblue,yellow,khaki4,grey)), org(hs), plot(true), wgraph_plot_opts([]), wgraph_plot_defs([]) ]. /** exp_gene_family_string_graph( +Exp, +Family, -Graph, +Opts ). exp_gene_family_string_graph( +Exp, +Family, ?DEPrs, ?NonDEPrs, -Graph, +Opts ). Generate and possibly plot the STRING graph of a known gene family as affected in a biological Exp_eriment. Each family gene is placed of the following states according to wether it was identified in Exp and how it was modified (in relation to background conditions): * Red = upregulated * Green = downregulated * Orange = either both directions or unknown direction * Grey = not identified Note that de-reguation trumps identification, that is, currently there is no distiction between genes that seen to be both significantly de-regulated and identified versus just those that are simply significantly de-regulated. In the exp_gene_family_string_graph/6 version DEPrs and NonDEPrs can be provided, which optimises use in loops over families (see exp_go_over_string_graphs/4). Opts * exp_ev_log(EvLog=true) are the expression values (ev) log values ? (also passed to bio_diffex/4) * faint_factor(Fctr=1.2) faint factor for non-significant nodes * include_non_present(IncP=true) false excludes non-indentified family genes * include_non_significant(IncS=true) false excluded non-significant family genes * node_colours(Clrs=clrs(red,green,yellow,khaki4,grey)) colours for the different types of nodes * org(Org=hs) organism in which Family is looked in (and experiment was performed) * org_exp_id(ExpID) the type of the experimental gene ids for the organism. default depends on Org, but currently all map to symb * plot(Plot=true) whether to plot the graph via wgraph_plot/2 * wgraph_plot_opts(WgOpts=[]) options for wgraph_plot/2 (in preference to any defaults from Self) * wgraph_plot_defs(WgDefs=[]) options for wgraph_plot/2 (added to the end, after any defaults from Self) These Options are passed to a number of other pack predicates. See [pack('bio_analytics/examples/bt.pl')]. == ?- lib(real), lib(mtx), absolute_file_name( pack('bio_analytics/data/silac/bt.csv'), CsvF ), Ppts = [ vjust= -1, node_size(3), mode="fruchtermanreingold", format(svg), stem(bt)], Opts = [ exp_ev_cut_let(inf), exp_ev_cut_get(-inf), include_non_present(false), include_non_significant(false), minw(200), wgraph_plot_opts(Ppts) ], exp_gene_family_string_graph( CsvF, autophagy, G, Opts ). == Produces file: bt.svg [[../doc/images/bt.svg]] @author nicos angelopoulos @version 0.1 2019/4/15 @see bio_diffex/4 @see gene_family/3 @see wgraph_plot/2 @see bio_symbols/3 */ exp_gene_family_string_graph( Exp, Fam, StGraph, Args ) :- exp_gene_family_string_graph( Exp, Fam, _DEPrs, _NonDEPrs, StGraph, Args ). exp_gene_family_string_graph( Exp, Fam, DEPrs, NonDEPrs, StGraph, Args ) :- options_append( exp_gene_family_string_graph, Args, Opts ), ( var(DEPrs) -> bio_diffex( Exp, DEPrs, NonDEPrs, Opts ) ; true ), options( org(Org), Opts ), gene_family( Fam, Org, Fymbs ), % sort( Fymbs, Oymbs ), options( exp_ev_log(EvLog), Opts ), ( EvLog == true -> Zero is 1; Zero is 0 ), exp_gene_family_string_graph_node_colours( Nlrs, Flrs, Opts ), options( include_non_present(IncP), Opts ), options( include_non_significant(IncS), Opts ), bio_symbols( DEPrs, DESymbPrs, Opts ), bio_symbols( NonDEPrs, NonDESymbPrs, Opts ), exp_gene_family_string_graph_nodes( Oymbs, DESymbPrs, NonDESymbPrs, Zero, Nlrs, Flrs, IncP, IncS, Nodes, NdClrs ), % % construct_graph( Oymbs, DEPrs, NonDEPrs, Graph, GraphWGOpts ), symbols_string_graph( Nodes, StGraphPrv, Opts ), options( wgraph_plot_opts(DomWGOpts), Opts ), options( wgraph_plot_defs(DefWGOpts), Opts ), EgfWGOpts = [colours(NdClrs),plotter(ggnet2)], flatten( [DomWGOpts,EgfWGOpts,DefWGOpts], WGOpts ), string_graph_single_edge_weight_adjusted( StGraphPrv, StGraph ), debug( exp_gene_family_string_graph(graph), 'Family: ~w, string graph: ~w', [Fam,StGraph] ), exp_wgraph_plot( StGraph, Fam, WGOpts ). exp_wgraph_plot( [], Fam, _WGOpts ) :- !, debug( ba(info), 'Empty string graph removed, for family: ~w', [Fam] ). % exp_wgraph_plot( [Node], Fam, _WGOpts ) :- % atomic(Node), % !, % debug( exp_gene_family_string_graph, 'Single node graph removed, for family: ~w', [Fam] ). exp_wgraph_plot( Graph, _Fam, Opts ) :- wgraph_plot( Graph, Opts ). string_graph_single_edge_weight_adjusted( Graph, Adjusted ) :- findall( W, member(_X-_Y:W,Graph), AllWs ), sort( AllWs, Ws ), % when therre is a single weight it should be in range 0-10 % as ggplot2 (and others i think) have difficult drawing reasonably widthed edges ( Ws = [_Single] -> maplist( string_graph_single_edge_weight_adjust_entry, Graph, Adjusted ) ; Adjusted = Graph ). string_graph_single_edge_weight_adjust_entry( X-Y:W, Edge ) :- Wadj is max(1, W // 500), Edge = X-Y:Wadj, !. string_graph_single_edge_weight_adjust_entry( Edge, Edge ). exp_gene_family_string_graph_nodes( [], _DEPrs, _NonDEPrs, _Zero, _Nlrs, _Flrs, _IncGrey, _IncS, [], [] ). exp_gene_family_string_graph_nodes( [Gn|Gns], DEPrs, NonDEPrs, Zero, Nlrs, Flrs, IncP, IncS, Nodes, NdClrs ) :- debug(exp_gene_family_string_graph(node), 'Gene node: ~w', [Gn] ), findall( Ev, member(Gn-Ev,DEPrs), Evs ), exp_gene_family_string_graph_nodes_de( Evs, Gn, Zero, NonDEPrs, Nlrs, Flrs, IncP, IncS, Nodes, NdClrs, TNodes, TNdClrs ), exp_gene_family_string_graph_nodes( Gns, DEPrs, NonDEPrs, Zero, Nlrs, Flrs, IncP, IncS, TNodes, TNdClrs ). exp_gene_family_string_graph_nodes_de( [], Gn, Zero, NonDEPrs, Nlrs, Flrs, IncP, IncS, Nodes, NdClrs, TNodes, TNdClrs ) :- findall( Ev, member(Gn-Ev,NonDEPrs), Evs ), ( Evs == [] -> ( IncP == false -> TNodes = Nodes, TNdClrs = NdClrs ; arg(5,Nlrs,Grey), Nodes = [Gn|TNodes], NdClrs = [Grey|TNdClrs] ) ; ( IncS == false -> TNodes = Nodes, TNdClrs = NdClrs ; Nodes = [Gn|TNodes], exp_gene_family_string_graph_nodes_de_direction( Evs, Zero, Dir ), arg( Dir, Flrs, NdClr ), NdClrs = [NdClr|TNdClrs] ) ). exp_gene_family_string_graph_nodes_de( [Ev|Evs], Gn, Zero, _NonDEPrs, Nlrs, _Flrs, _IncP, _IncS, Nodes, NdClrs, TNodes, TNdClrs ) :- exp_gene_family_string_graph_nodes_de_direction( [Ev|Evs], Zero, Dir ), arg( Dir, Nlrs, NdClr ), Nodes = [Gn|TNodes], NdClrs = [NdClr|TNdClrs]. exp_gene_family_string_graph_nodes_de_direction( Evs, Zero, Dir ) :- partition( <(Zero), Evs, More, LessOrEqual ), ( More == [] -> ( LessOrEqual == [] -> throw( directionless(Evs) ) ; Dir is 2 ) ; ( LessOrEqual == [] -> Dir is 1 ; Dir is 3 ) ). /* construct_graph( [], _DEPrs, _NonDEPrs, [], GraphWGOpts ) :- construct_graph( [Gn|Gns], DEPrs, NonDEPrs, Graph, GraphWGOpts ) :- findall( Ev, member(Gn-Ev,DEPrs), Evs ), */ exp_gene_family_string_graph_node_colours( NdClrs, FtClrs, Opts ) :- options( node_colours(NdClrs), Opts ), options( faint_factor(Fctr), Opts ), NdClrs =.. [NcName|ClrsL], col_faint( ClrsL, Fctr, FaintsL ), FtClrs =.. [NcName|FaintsL].