//CYTOSCAPE SCRIPT
private static string get_script(int feature_count, IGoAnalysis quantitative, string node_position, string edges_path, string nodes_path, string styles_path, string style_name)
{
double sleep_factor = feature_count / 1000;
string node_column_types = quantitative != null ? "s,s,d,s,i,d,d,boolean,s" : "s,s,d,s,i"; //Cytoscape bug: "b" doesn't work in 3.4.0, only "boolean" does
string edge_column_types = "s,s,s,s,s";
return(string.Join(Environment.NewLine, new string[] {
//Load Tables
"network import file file=\"" + edges_path + "\" firstRowAsColumnNames=true delimiters=\"\\t\" indexColumnSourceInteraction=\"1\" indexColumnTargetInteraction=\"3\" startLoadRow=\"0\" dataTypeList=\"" + edge_column_types + "\"",
"command sleep duration=" + (0.8 + Math.Round((1.0 * sleep_factor), 2)).ToString(),
"table import file file=\"" + nodes_path + "\" startLoadRow=\"0\" keyColumnIndex=\"1\" DataTypeTargetForNetworkCollection=\"Node Table Columns\" dataTypeList=\"" + node_column_types + "\"",
"command sleep duration=" + (0.5 + Math.Round((0.5 * sleep_factor), 2)).ToString(),
//Load Settings
"vizmap load file file=\"" + styles_path + "\"",
"command sleep duration=" + (1.0 + Math.Round((1.0 * sleep_factor), 2)).ToString(),
Lollipop.node_positioning.ToList().IndexOf(node_position) == 0 ? "layout degree-circle" : "layout attribute-circle NodeAttribute=" + layout_header,
"command sleep duration=" + (0.5 + Math.Round((0.5 * sleep_factor), 2)).ToString(),
"view fit content",
//Mash applying the style because it flakes out
"command sleep duration=1",
"vizmap apply styles=\"" + style_name + "\"",
"command sleep duration=1",
"vizmap apply styles=\"" + style_name + "\"",
"command sleep duration=1",
"vizmap apply styles=\"" + style_name + "\"",
}));
}
public DisplayQuantitativeValues(QuantitativeProteoformValues q, IGoAnalysis analysis)
: base(q)
{
proteoform = q.proteoform;
qval = q;
this.analysis = analysis;
}
public override void reestablishSignficance(IGoAnalysis analysis)
{
if (!Sweet.lollipop.useLocalFdrCutoff)
{
relativeDifferenceFDR = computeRelativeDifferenceFDR(avgSortedPermutationRelativeDifferences, sortedProteoformRelativeDifferences, Sweet.lollipop.satisfactoryProteoforms, flattenedPermutedRelativeDifferences, Sweet.lollipop.offsetTestStatistics);
}
else
{
Parallel.ForEach(Sweet.lollipop.satisfactoryProteoforms, eP => { eP.quant.TusherValues2.significant = eP.quant.TusherValues2.roughSignificanceFDR <= Sweet.lollipop.localFdrCutoff; });
}
inducedOrRepressedProteins = Sweet.lollipop.getInducedOrRepressedProteins(Sweet.lollipop.satisfactoryProteoforms.Where(pf => pf.quant.TusherValues2.significant), GoAnalysis);
}
public static string write_cytoscape_script(List <ProteoformFamily> families, List <ProteoformFamily> all_families,
string folder_path, string file_prefix, string time_stamp,
IGoAnalysis quantitative, bool quantitative_redBorder, bool quantitative_boldFace,
string color_scheme, string edge_label, string node_label, string node_label_position, string node_position, int double_rounding,
bool gene_centric_families, string prefered_gene_label)
{
return(write_script(families, all_families,
folder_path, file_prefix, time_stamp,
quantitative, quantitative_redBorder, quantitative_boldFace,
color_scheme, edge_label, node_label, node_label_position, node_position, double_rounding,
gene_centric_families, prefered_gene_label, false));
}
private static string write_script(List <ProteoformFamily> families, List <ProteoformFamily> all_families,
string folder_path, string file_prefix, string time_stamp,
IGoAnalysis quantitative, bool quantitative_redBorder, bool quantitative_boldFace,
string color_scheme, string edge_label, string node_label, string node_label_position, string node_position, int double_rounding,
bool gene_centric_families, string preferred_gene_label, bool scale_node_size)
{
//Check if valid folder
if (folder_path == "" || !Directory.Exists(folder_path))
{
return("Please choose a folder in which the families will be built, so you can load them into Cytoscape.");
}
if (families.Any(f => f.experimental_proteoforms.Count == 0))
{
return("Error: there is a family with zero experimental proteoforms.");
}
string nodes_path = Path.Combine(folder_path, file_prefix + node_file_prefix + time_stamp + node_file_extension);
string edges_path = Path.Combine(folder_path, file_prefix + edge_file_prefix + time_stamp + edge_file_extension);
string styles_path = Path.Combine(folder_path, file_prefix + style_file_prefix + time_stamp + style_file_extension);
string script_path = Path.Combine(folder_path, file_prefix + script_file_prefix + time_stamp + script_file_extension);
string style_name = "ProteoformFamilies" + time_stamp;
IEnumerable <TheoreticalProteoform> theoreticals = families.SelectMany(f => f.theoretical_proteoforms);
//Dictionary<string, GeneName> gene_dict = new Dictionary<string, GeneName>();
//if (gene_centric_families)
// foreach (TheoreticalProteoform t in theoreticals)
// {
// string preferred = t.gene_name.get_prefered_name(prefered_gene_label);
// if (gene_dict.ContainsKey(preferred)) gene_dict[preferred].merge(t.gene_name);
// else gene_dict.Add(preferred, t.gene_name);
// }
string script = get_script(families.Sum(f => f.proteoforms.Count() + f.relations.Count), quantitative, node_position, edges_path, nodes_path, styles_path, style_name);
string node_table = get_cytoscape_nodes_tsv(families, quantitative, color_scheme, node_label, node_label_position, node_position, double_rounding, theoreticals, gene_centric_families, preferred_gene_label);
string edge_table = get_cytoscape_edges_tsv(families, edge_label, node_label, double_rounding, theoreticals, gene_centric_families, preferred_gene_label);
File.WriteAllText(edges_path, edge_table);
File.WriteAllText(nodes_path, node_table);
File.WriteAllText(script_path, script);
write_styles(scale_node_size ? families : all_families, styles_path, style_name, time_stamp,
edge_label, node_label, node_label_position, color_scheme, quantitative, quantitative_redBorder, quantitative_boldFace);
string selected_family_string = "Finished building selected famil";
selected_family_string += families.Count == 1 ? "y :" : "ies :#";
selected_family_string += (families.Count <= 3) ? string.Join(", #", families.Select(f => f.family_id)) : string.Join(", #", families.Select(f => f.family_id).ToList().Take(3)) + ", etc.";
return(selected_family_string + ".\n\nPlease load them into Cytoscape 3.0 or later using \"Tools\" -> \"Execute Command File\" and choosing the script_[TIMESTAMP].txt file in your specified directory.");
}
public static string write_cytoscape_script(object[] stuff, List <ProteoformFamily> all_families,
string folder_path, string file_prefix, string time_stamp,
IGoAnalysis quantitative, bool quantitative_redBorder, bool quantitative_boldFace,
string color_scheme, string edge_label, string node_label, string node_label_position, string node_position, int double_rounding,
bool gene_centric_families, string prefered_gene_label, bool scale_node_size)
{
List <ProteoformFamily> families = stuff.OfType <ProteoformFamily>().ToList();
if (stuff.Length <= 0)
{
return("No objects were selected");
}
if (families.Count <= 0 && typeof(TheoreticalProteoform).IsAssignableFrom(stuff[0].GetType()))
{
families = get_families(stuff.OfType <TheoreticalProteoform>(), all_families).Distinct().ToList();
}
if (families.Count <= 0 && typeof(GoTerm) == stuff[0].GetType())
{
families = get_families(stuff.OfType <GoTerm>(), all_families).Distinct().ToList();
}
if (families.Count <= 0 && typeof(GoTermNumber) == stuff[0].GetType())
{
families = get_families(stuff.OfType <GoTermNumber>(), all_families).Distinct().ToList();
}
if (families.Count <= 0 && typeof(QuantitativeProteoformValues).IsAssignableFrom(stuff[0].GetType()))
{
families = get_families(stuff.OfType <QuantitativeProteoformValues>(), all_families).Distinct().ToList();
}
if (families.Count <= 0)
{
return("Selected objects were not recognized.");
}
return(write_script(families, all_families,
folder_path, file_prefix, time_stamp,
quantitative, quantitative_redBorder, quantitative_boldFace,
color_scheme, edge_label, node_label, node_label_position, node_position, double_rounding,
gene_centric_families, prefered_gene_label, scale_node_size));
}
public static void write_styles(List <ProteoformFamily> all_families, string styles_path, string style_name, string time_stamp,
string edge_label, string node_label, string node_label_position, string color_scheme,
IGoAnalysis quantitative, bool quantitative_redBorder, bool quantitative_boldFace)
{
XmlWriterSettings xmlWriterSettings = new XmlWriterSettings()
{
Indent = true,
IndentChars = " "
};
using (XmlWriter writer = XmlWriter.Create(styles_path, xmlWriterSettings))
{
writer.WriteStartDocument();
writer.WriteStartElement("vizmap");
writer.WriteAttributeString("documentVersion", "3.0");
writer.WriteAttributeString("id", time_stamp);
writer.WriteStartElement("visualStyle");
writer.WriteAttributeString("name", style_name);
//NETWORK PROPERTIES
writer.WriteStartElement("network");
IEnumerable <KeyValuePair <string, string> > default_network_styles = default_styles.Where(n => n.Key.StartsWith("NETWORK"));
foreach (KeyValuePair <string, string> style in default_network_styles)
{
writer.WriteStartElement("visualProperty");
writer.WriteAttributeString("name", style.Key);
writer.WriteAttributeString("default", style.Value);
writer.WriteEndElement();
}
writer.WriteEndElement();
//NODE PROPERTIES
double max_total_intensity = all_families.SelectMany(f => f.experimental_proteoforms.Where(e => !e.topdown_id)).Count() > 0 ? quantitative != null ?
(double)all_families.SelectMany(f => f.experimental_proteoforms).Max(p => p.quant.intensitySum) :
all_families.SelectMany(f => f.experimental_proteoforms).Max(p => p.agg_intensity) : 1e6;
writer.WriteStartElement("node");
writer.WriteStartElement("dependency");
writer.WriteAttributeString("name", "nodeCustomGraphicsSizeSync");
writer.WriteAttributeString("value", "true");
writer.WriteEndElement();
writer.WriteStartElement("dependency");
writer.WriteAttributeString("name", "nodeSizeLocked");
writer.WriteAttributeString("value", "true");
writer.WriteEndElement();
IEnumerable <KeyValuePair <string, string> > default_node_styles = default_styles.Where(n => n.Key.StartsWith("NODE") || n.Key.StartsWith("COMPOUND_NODE"));
foreach (KeyValuePair <string, string> style in default_node_styles)
{
writer.WriteStartElement("visualProperty");
writer.WriteAttributeString("name", style.Key);
//Defaults
if (style.Key == "NODE_LABEL_POSITION")
{
if (node_label_position == node_label_positions[1])
{
writer.WriteAttributeString("default", "N,S,c,0.00,0.00");
}
else if (node_label_position == node_label_positions[2])
{
writer.WriteAttributeString("default", "S,N,c,0.00,0.00");
}
writer.WriteEndElement();
continue;
}
else
{
writer.WriteAttributeString("default", style.Value);
}
//Discrete and continuous mapping
if (style.Key == "NODE_FILL_COLOR")
{
write_discreteMapping(writer, "string", proteoform_type_header, new List <Tuple <string, string> >()
{
new Tuple <string, string>(quantitative != null ? "#FFFFFF" : color_schemes[color_scheme][0], experimental_label),
new Tuple <string, string>(not_quantified, experimental_notQuantified_label),
new Tuple <string, string>(color_schemes[color_scheme][1], modified_theoretical_label),
new Tuple <string, string>(color_schemes[color_scheme][2], unmodified_theoretical_label),
new Tuple <string, string>(color_schemes[color_scheme][6], td_label),
new Tuple <string, string>(color_schemes[color_scheme][4], gene_name_label)
//new Tuple<string, string>(color_schemes[color_scheme][4], transcript_name_label)
});
}
if (style.Key == "NODE_SHAPE")
{
write_discreteMapping(writer, "string", proteoform_type_header, new List <Tuple <string, string> >()
{
new Tuple <string, string>("ELLIPSE", experimental_label),
new Tuple <string, string>("ELLIPSE", experimental_notQuantified_label),
new Tuple <string, string>("ELLIPSE", modified_theoretical_label),
new Tuple <string, string>("ELLIPSE", unmodified_theoretical_label),
new Tuple <string, string>("RECTANGLE", gene_name_label)
//new Tuple<string, string>("DIAMOND", transcript_name_label)
});
}
if (style.Key == "NODE_LABEL_FONT_FACE")
{
write_discreteMapping(writer, "string", proteoform_type_header, new List <Tuple <string, string> >()
{
new Tuple <string, string>("Arial Italic,plain,14", gene_name_label),
new Tuple <string, string>("Arial,plain,14", modified_theoretical_label),
new Tuple <string, string>("Arial,plain,14", unmodified_theoretical_label),
new Tuple <string, string>("Arial,plain,14", experimental_label),
new Tuple <string, string>("Arial,plain,14", experimental_notQuantified_label)
});
}
if (style.Key == "NODE_LABEL_COLOR")
{
write_passthrough(writer, "string", "shared name");
}
if (style.Key == "NODE_LABEL")
{
write_passthrough(writer, "string", "name");
}
if (style.Key == "NODE_SIZE")
{
write_continuousMapping(writer, "float", size_header, new List <Tuple <string, string, string, string> >()
{
new Tuple <string, string, string, string>("1.0", "20.0", "20.0", "1.0"),
new Tuple <string, string, string, string>("300.0", "1.0", "300.0", max_total_intensity.ToString()) //max node size should be set to the total intensity of the proteoform
});
}
if (style.Key == "NODE_CUSTOMGRAPHICS_1" && quantitative != null)
{
write_passthrough(writer, "string", piechart_header);
}
if (style.Key == "NODE_BORDER_WIDTH" && quantitative != null && quantitative_redBorder)
{
write_discreteMapping(writer, "boolean", significant_header, new List <Tuple <string, string> >()
{
new Tuple <string, string>("7.0", "True")
});
}
if (style.Key == "NODE_BORDER_PAINT" && quantitative != null && quantitative_redBorder)
{
write_discreteMapping(writer, "boolean", significant_header, new List <Tuple <string, string> >()
{
new Tuple <string, string>("#FFFFFF", "False"),
new Tuple <string, string>(color_schemes[color_scheme][5], "True")
});
}
if (style.Key == "NODE_BORDER_TRANSPARENCY" && quantitative != null && quantitative_redBorder)
{
write_discreteMapping(writer, "boolean", significant_header, new List <Tuple <string, string> >()
{
new Tuple <string, string>("255", "True"),
});
}
if (style.Key == "NODE_LABEL_FONT_FACE" && quantitative != null && quantitative_boldFace)
{
write_discreteMapping(writer, "boolean", significant_header, new List <Tuple <string, string> >()
{
new Tuple <string, string>("Dialog.bold,plain,14", "True"),
});
}
if (style.Key == "NODE_TOOLTIP")
{
write_passthrough(writer, "string", tooltip_header);
}
writer.WriteEndElement();
}
writer.WriteEndElement();
//EDGE PROPERTIES
writer.WriteStartElement("edge");
writer.WriteStartElement("dependency");
writer.WriteAttributeString("name", "arrowColorMatchesEdge");
writer.WriteAttributeString("value", "false");
writer.WriteEndElement();
IEnumerable <KeyValuePair <string, string> > default_edge_styles = default_styles.Where(n => n.Key.StartsWith("EDGE"));
foreach (KeyValuePair <string, string> style in default_edge_styles)
{
writer.WriteStartElement("visualProperty");
writer.WriteAttributeString("name", style.Key);
writer.WriteAttributeString("default", style.Value);
if (style.Key == "EDGE_LABEL" && edge_label == Lollipop.edge_labels[0])
{
write_passthrough(writer, "string", delta_mass_header);
}
if (style.Key == "EDGE_LABEL" && edge_label == Lollipop.edge_labels[1])
{
write_passthrough(writer, "string", edge_ptm_header);
}
writer.WriteEndElement();
}
writer.WriteEndElement();
//OTHER PROPERTIES
// none, currently
writer.WriteEndElement();
writer.WriteEndElement();
writer.WriteEndDocument();
}
}
public static string get_cytoscape_nodes_tsv(List <ProteoformFamily> families,
IGoAnalysis quantitative,
string color_scheme, string node_label, string node_label_position, string node_position, int double_rounding,
IEnumerable <TheoreticalProteoform> theoreticals, bool gene_centric_families, string preferred_gene_label)
{
DataTable node_table = new DataTable();
node_table.Columns.Add("accession", typeof(string));
node_table.Columns.Add(proteoform_type_header, typeof(string));
node_table.Columns.Add(size_header, typeof(double));
node_table.Columns.Add(tooltip_header, typeof(string));
node_table.Columns.Add(layout_header, typeof(int));
if (quantitative != null)
{
node_table.Columns.Add(Sweet.lollipop.numerator_condition, typeof(string));
node_table.Columns.Add(Sweet.lollipop.denominator_condition, typeof(string));
node_table.Columns.Add(significant_header, typeof(string));
node_table.Columns.Add(piechart_header, typeof(string));
}
//Choose the layout order
IEnumerable <Proteoform> layout_order;
switch (Lollipop.node_positioning.ToList().IndexOf(node_position))
{
case 0: //arbitrary circle
case 2: //mass circle
default:
layout_order = families.SelectMany(f => f.experimental_proteoforms).OfType <Proteoform>().Concat(theoreticals).OrderBy(p => p.modified_mass);
break;
case 1: //mass-based spiral
layout_order = theoreticals.OrderByDescending(p => p.modified_mass).OfType <Proteoform>().Concat(families.SelectMany(f => f.experimental_proteoforms).OfType <Proteoform>().OrderBy(p => p.modified_mass));
break;
}
int layout_rank = 1;
string node_rows = "";
foreach (Proteoform p in layout_order.ToList())
{
if (p as TheoreticalProteoform != null)
{
string node_type = String.Equals(p.ptm_set.ptm_description, "unmodified", StringComparison.CurrentCultureIgnoreCase) ? unmodified_theoretical_label : modified_theoretical_label;
node_table.Rows.Add(get_proteoform_shared_name(p, node_label, double_rounding), node_type, mock_intensity, "", layout_rank);
}
if (p as ExperimentalProteoform != null)
{
ExperimentalProteoform ep = p as ExperimentalProteoform;
string node_type = quantitative != null && ep.quant.intensitySum == 0 ?
experimental_notQuantified_label :
quantitative == null && ep.topdown_id ?
td_label :
experimental_label;
string total_intensity = quantitative != null ?
ep.quant.intensitySum == 0 ? mock_intensity : ((double)ep.quant.intensitySum).ToString() :
ep.agg_intensity == 0 ? mock_intensity : ep.agg_intensity.ToString();
//Names and size
node_rows += string.Join("\t", new List <string> {
get_proteoform_shared_name(p, node_label, double_rounding), node_type, total_intensity
});
//Set tooltip information
string tooltip = string.Join("; ", new string[]
{
"Accession = " + p.accession.ToString(),
"Aggregated Mass = " + ep.agg_mass.ToString(),
"Aggregated Retention Time = " + ep.agg_rt.ToString(),
"Total Intensity = " + total_intensity.ToString(),
"Aggregated Component Count = " + (ep.topdown_id ? (ep as TopDownProteoform).topdown_hits.Count.ToString() : ep.aggregated.Count.ToString()),
Sweet.lollipop.neucode_labeled ? "; Lysine Count = " + p.lysine_count : "",
"Abundant Component for Manual Validation of Identification: " + ep.manual_validation_id,
"Abundant Component for Manual Validation of Identification Validation: " + ep.manual_validation_verification
});
if (quantitative != null && ep.quant.intensitySum > 0)
{
tooltip += "\\n\\nQuantitation Results:" +
string.Join("; ", new string[] {
"Q-Value = " + (quantitative as TusherAnalysis1 != null ? ep.quant.TusherValues1.roughSignificanceFDR.ToString() : quantitative as TusherAnalysis2 != null ? ep.quant.TusherValues2.roughSignificanceFDR.ToString() : ""),
"Log2FC = " + (quantitative as Log2FoldChangeAnalysis != null ? ep.quant.Log2FoldChangeValues.logfold2change.ToString() : ep.quant.tusherlogFoldChange.ToString()),
"Significant = " + (quantitative as TusherAnalysis1 != null ? ep.quant.TusherValues1.significant.ToString() : quantitative as TusherAnalysis2 != null ? ep.quant.TusherValues2.significant.ToString() : quantitative as Log2FoldChangeAnalysis != null ? ep.quant.Log2FoldChangeValues.significant.ToString() : ""),
Sweet.lollipop.numerator_condition + " Quantitative Component Count = " + ep.lt_quant_components.Count.ToString(),
Sweet.lollipop.denominator_condition + " Quantitative Component Count = " + ep.hv_quant_components.Count.ToString(),
"Abundant Component for Manual Validation of Quantification: " + ep.manual_validation_quant
});
}
if (quantitative as TusherAnalysis1 != null && ep.quant.intensitySum != 0)
{
node_table.Rows.Add(get_proteoform_shared_name(p, node_label, double_rounding), node_type, total_intensity, tooltip, layout_rank, ((double)ep.quant.TusherValues1.numeratorIntensitySum).ToString(), ((double)ep.quant.TusherValues1.denominatorIntensitySum).ToString(), ep.quant.TusherValues1.significant.ToString(), get_piechart_string(color_scheme));
}
else if (quantitative as TusherAnalysis2 != null && ep.quant.intensitySum != 0)
{
node_table.Rows.Add(get_proteoform_shared_name(p, node_label, double_rounding), node_type, total_intensity, tooltip, layout_rank, ((double)ep.quant.TusherValues2.numeratorIntensitySum).ToString(), ((double)ep.quant.TusherValues2.denominatorIntensitySum).ToString(), ep.quant.TusherValues2.significant.ToString(), get_piechart_string(color_scheme));
}
else if (quantitative as Log2FoldChangeAnalysis != null && ep.quant.intensitySum != 0)
{
node_table.Rows.Add(get_proteoform_shared_name(p, node_label, double_rounding), node_type, total_intensity, tooltip, layout_rank, ep.quant.Log2FoldChangeValues.allIntensities.Where(kv => kv.Value.condition == Sweet.lollipop.induced_condition).Sum(kv => kv.Value.intensity_sum).ToString(), ep.quant.Log2FoldChangeValues.allIntensities.Where(kv => kv.Value.condition != Sweet.lollipop.induced_condition).Sum(kv => kv.Value.intensity_sum).ToString(), ep.quant.Log2FoldChangeValues.significant.ToString(), get_piechart_string(color_scheme));
}
else if (quantitative != null)
{
node_table.Rows.Add(get_proteoform_shared_name(p, node_label, double_rounding), node_type, total_intensity, tooltip, layout_rank, "", "", "", "");
}
else
{
node_table.Rows.Add(get_proteoform_shared_name(p, node_label, double_rounding), node_type, total_intensity, tooltip, layout_rank);
}
}
layout_rank++;
}
if (gene_centric_families)
{
foreach (string gene_name in theoreticals.Select(t => t.gene_name.get_prefered_name(preferred_gene_label)).ToList().
Concat(families.SelectMany(f => f.experimental_proteoforms.Where(pf => pf.topdown_id)).
Select(t => t.gene_name.get_prefered_name(preferred_gene_label))).Distinct())
{
if (gene_name != null && quantitative != null)
{
node_table.Rows.Add(gene_name, gene_name_label, mock_intensity, "Other Gene Names: ", 0, "", "", "", "");
}
else if (gene_name != null)
{
node_table.Rows.Add(gene_name, gene_name_label, mock_intensity, "Other Gene Names: ", 0);
}
}
}
return(get_table_string(node_table));
}
public abstract void reestablishSignficance(IGoAnalysis analysis);
