# HG changeset patch # User bornea # Date 1462978756 14400 # Node ID f3fcab0e9edd0d17e89c5b894d6d8bb023f1f2a9 # Parent 8f463e2a34d59645c4093aa4914390eba7e48cd2 Uploaded diff -r 8f463e2a34d5 -r f3fcab0e9edd APOSTL_Static_Bubblegraph_Generator.xml --- a/APOSTL_Static_Bubblegraph_Generator.xml Wed May 11 10:59:06 2016 -0400 +++ b/APOSTL_Static_Bubblegraph_Generator.xml Wed May 11 10:59:16 2016 -0400 @@ -1,6 +1,6 @@ - APOSTL_Static_Bubblegraph_Generator.py $list_file $prey_file $crapome $color $label $cutoff $type $inc_file $exc_file $outfile $NSAF_zoom $SAINT_zoom $SAINT $NSAF \$INSTALL_RUN_PATH/ + APOSTL_Static_Bubblegraph_Generator.py $list_file $prey_file $crapome $inter $main_x $main_y $size_id $color $SS_cutoff $FC_cutoff $NS_cutoff $theme $label $label_color $bubble_color $outline_color $filt_color $outfile \$INSTALL_RUN_PATH/ INSTALL_RUN_PATH @@ -12,26 +12,2094 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - 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- - - - - + + - + + @@ -43,89 +2111,5 @@ -Post-processing: -Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things: - -APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait - -OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome - -Bubble graphs are generated for each bait where: - -- x axis is the natural log of the NSAF values - -- y axis is the observed log2 fold change (as compared to control) - -- bubble radius is proportional to the average observed spectra - -OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan - -APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option. - -INPUTS: - -List File: - -- SAINTexpress generated "list.txt" file - -Prey File: - -- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress - -Crapome File: - -- raw output from Crapome Workflow 1 query (http://www.crapome.org) - -Color: - -- Specify the color of the bubbles within the graph. - -- If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity - -Use labels: - -- Adds gene name labels to bubbles within the "zoomed in" graphs -SAINT Score Cutoff: - -- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8) - -- Also used for filtering during the generation of the cytoscape network - -Species: - -- Human, mouse, or yeast - -Interaction Confidence: - -- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database - -- Suggestions: - -* low: 0 - -* medium: 0.5 - -* high: 0.7 - -* very high: 0.9 - -OUTPUTS: - -Bubble Graphs: - -- Unfiltered Data: - -* NSAF v. Log2(FoldChange) - -* SAINTscore v. Log2(FoldChange) - -- Filtered by SAINT Score - -* NSAF v. Log2(FoldChange) - -* SAINTscore v. Log2(FoldChange) - -Output.txt -- SAINTexpress "list.txt" output with additional columns that were used during the analysis