visualization stuff

smith-chem-wisc · Feb 25, 2019 · 0062213 · 0062213
1 parent 14e7509
commit 0062213
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Showing 6 changed files with 35 additions and 22 deletions.
diff --git a/ProteoformSuiteGUI/ExperimentExperimentComparison.cs b/ProteoformSuiteGUI/ExperimentExperimentComparison.cs
@@ -139,7 +139,7 @@ public void InitializeParameterSet()
             xMinEE.Value = 0; // scaling for x-axis minimum in the histogram of all EE pairs
 
             nUD_PeakWidthBase.Minimum = 0.001m;
-            nUD_PeakWidthBase.Maximum = 1;
+            nUD_PeakWidthBase.Maximum = 10;
             nUD_PeakWidthBase.Value = Convert.ToDecimal(Sweet.lollipop.peak_width_base_ee);
 
             nUD_PeakCountMinThreshold.ValueChanged -= nUD_PeakCountMinThreshold_ValueChanged;

diff --git a/ProteoformSuiteGUI/ProteoformFamilies.Designer.cs b/ProteoformSuiteGUI/ProteoformFamilies.Designer.cs
diff --git a/ProteoformSuiteGUI/ProteoformFamilies.cs b/ProteoformSuiteGUI/ProteoformFamilies.cs
@@ -330,7 +330,7 @@ private void btn_buildSelectedFamilies_Click(object sender, EventArgs e)
                 Sweet.lollipop.family_build_folder_path, "", time_stamp,
                 cb_buildAsQuantitative.Checked ? (MdiParent as ProteoformSweet).resultsSummary.get_go_analysis() : null, cb_redBorder.Checked, cb_boldLabel.Checked,
                 cmbx_colorScheme.SelectedItem.ToString(), cmbx_edgeLabel.SelectedItem.ToString(), cmbx_nodeLabel.SelectedItem.ToString(), cmbx_nodeLabelPositioning.SelectedItem.ToString(), cmbx_nodeLayout.SelectedItem.ToString(), Sweet.lollipop.deltaM_edge_display_rounding,
-                cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString());
+                cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString(), cb_scale_nodes.Checked);
             MessageBox.Show(message, "Cytoscape Build");
         }
 

diff --git a/ProteoformSuiteGUI/Quantification.cs b/ProteoformSuiteGUI/Quantification.cs
@@ -1245,7 +1245,7 @@ private void btn_buildSelectedQuantFamilies_Click(object sender, EventArgs e)
             string message = CytoscapeScript.write_cytoscape_script(selected, Sweet.lollipop.target_proteoform_community.families,
                 Sweet.lollipop.family_build_folder_path, "", time_stamp, get_go_analysis(), cb_redBorder.Checked, cb_boldLabel.Checked,
                 cmbx_colorScheme.SelectedItem.ToString(), cmbx_edgeLabel.SelectedItem.ToString(), cmbx_nodeLabel.SelectedItem.ToString(), cmbx_nodeLabelPositioning.SelectedItem.ToString(), cmbx_nodeLayout.SelectedItem.ToString(), Sweet.lollipop.deltaM_edge_display_rounding,
-                cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString());
+                cb_geneCentric.Checked, cmbx_geneLabel.SelectedItem.ToString(), false);
             MessageBox.Show(message, "Cytoscape Build");
         }
 

diff --git a/ProteoformSuiteInternal/CytoscapeScript.cs b/ProteoformSuiteInternal/CytoscapeScript.cs
@@ -82,14 +82,14 @@ public static string write_cytoscape_script(List<ProteoformFamily> families, Lis
                 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);
+                gene_centric_families, prefered_gene_label, false);
         }
 
         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 gene_centric_families, string prefered_gene_label, bool scale_node_size)
         {
             List<ProteoformFamily> families = stuff.OfType<ProteoformFamily>().ToList();
 
@@ -108,7 +108,7 @@ public static string write_cytoscape_script(object[] stuff, List<ProteoformFamil
                 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);
+                gene_centric_families, prefered_gene_label, scale_node_size);
         }
 
         #endregion CYTOSCAPE SCRIPT Public Methods
@@ -119,7 +119,7 @@ private static string write_script(List<ProteoformFamily> families, List<Proteof
             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 gene_centric_families, string preferred_gene_label, bool scale_node_size)
         {
             //Check if valid folder
             if (folder_path == "" || !Directory.Exists(folder_path))
@@ -150,7 +150,7 @@ private static string write_script(List<ProteoformFamily> families, List<Proteof
             File.WriteAllText(edges_path, edge_table);
             File.WriteAllText(nodes_path, node_table);
             File.WriteAllText(script_path, script);
-            write_styles(all_families, styles_path, style_name, time_stamp,
+            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";

diff --git a/ProteoformSuiteInternal/ResultsSummaryGenerator.cs b/ProteoformSuiteInternal/ResultsSummaryGenerator.cs
@@ -79,7 +79,7 @@ private static void save_cytoscripts(string directory, string timestamp, IGoAnal
                     directory, gtn.Aspect.ToString() + gtn.Description.Replace(" ", "_").Replace(@"\", "_").Replace(@"/", "_") + "_", timestamp,
                     go_analysis as IGoAnalysis, true, true,
                     CytoscapeScript.color_scheme_names[1], Lollipop.edge_labels[1], Lollipop.node_labels[1], CytoscapeScript.node_label_positions[0], Lollipop.node_positioning[1], 2,
-                    Lollipop.gene_centric_families, Lollipop.preferred_gene_label);
+                    Lollipop.gene_centric_families, Lollipop.preferred_gene_label, false);
                 message += Environment.NewLine;
             }
             message += "Remember to install the package \"enhancedGraphics\" under App -> App Manager to view piechart nodes for quantitative data";