# HG changeset patch # User bornea # Date 1463605022 14400 # Node ID 33e9cdd6bbe88bf5156a9e41609dbc9a487901f2 # Parent ed4d14e83f445512a8decbae92dae72f217177b9 Uploaded diff -r ed4d14e83f44 -r 33e9cdd6bbe8 APOSTL_Static_Bubblegraph_Generator.xml --- a/APOSTL_Static_Bubblegraph_Generator.xml Wed May 18 16:56:23 2016 -0400 +++ b/APOSTL_Static_Bubblegraph_Generator.xml Wed May 18 16:57:02 2016 -0400 @@ -1,34 +1,1429 @@ - 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 + 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 + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - + + - + + @@ -40,89 +1435,96 @@ -Post-processing: -Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things: +Bubble Graph Generator +^^^^^^^^^^^^^^^^^^^^^^ -APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait +This Bubble Graph Generator is a static version of the APOSTL interactive affinity proteomics analysis +software developed to reformat affinity proteomics data (both spectral counting and MS1) for input +into the SAINTexpress statistical package and to visualize the output(s). APOSTL was developed at +H. Lee Moffitt Cancer Center and Research Institute and distributed under a GNU General Public License (GPL). -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 +**1) SAINT Output File** -- y axis is the observed log2 fold change (as compared to control) +SAINTexpress generated *list.txt* file. -- bubble radius is proportional to the average observed spectra + **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g. + "EGFR\_HUMAN" or "P00533"). -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 +**2) Prey File** -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. +Please specify a *Prey* file for Bubble Graph creation. A *Prey* file +should contain three columns: prey (protein) name, prey amino acid +length, and prey gene name (no header). -INPUTS: - -List File: +**3) CRAPome File** -- SAINTexpress generated "list.txt" file +Please specify an *CRAPome* file for Bubble Graph creation. An *CRAPome* +file should contain five columns: IP name, Mapped Gene Symbol, Number of +Experiments (ratio), and Average spectral counts, and Max spectral counts. -Prey File: - -- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress +**4) Interactions File** -Crapome File: +Please specify an *Inter* file for Bubble Graph creation. An *Inter* +file should contain four columns: IP name, bait name, prey name, and +spectral counts or intensity values, depending on the mode of +quantification. -- raw output from Crapome Workflow 1 query (http://www.crapome.org) - -Color: +**5) X Axis Label** -- Specify the color of the bubbles within the graph. +Select the value to be used as the X axis in the Bubble Graph. + +**6) Y Axis Label** -- If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity +Selct the value to be used as the Y axis in the Bubble Graph. -Use labels: +**7) Bubble Size** -- Adds gene name labels to bubbles within the "zoomed in" graphs -SAINT Score Cutoff: +Select the value to size the bubbles in the Bubble Graph. The "fixed" +option will make all the bubbles the same size -- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8) +**8) Color** -- Also used for filtering during the generation of the cytoscape network +Crapome will color the bubbles acooring to their likelyhood of a good +interaction. Fixed will make all the bubbles one color (must be used if no-crapome +file is provided). -Species: - -- Human, mouse, or yeast +**9) SAINT Score Cutoff** -Interaction Confidence: +SaintScore filter in range 0-1 (default 0.8) -- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database +**10) Fold Change Cutoff** -- Suggestions: +Fold Change filter in range -Inf to Inf (default 0) -* low: 0 +**11) NSAF Score Cutoff** -* medium: 0.5 +NSAF Score filter in range -Inf to Inf (default 0) -* high: 0.7 +**12) Plot Theme** -* very high: 0.9 +Select theme to be used when creating Bubble Graph. -OUTPUTS: +**13) Label Type** -Bubble Graphs: +Select the type of labeling: no labels, label points greater than CRAPomePCT cutoff, and +all bubbles labeled. -- Unfiltered Data: +**14) Label Color** -* NSAF v. Log2(FoldChange) +Select label color. -* SAINTscore v. Log2(FoldChange) +**15) Bubble Color** -- Filtered by SAINT Score +Select color of Bubble interior. If *Color* is set to *crapome* this will act as the color of CRAPomePCT greater than 80. If *Color* is set to *fixed* this will be the bubble color. -* NSAF v. Log2(FoldChange) +**16) Outline Color** -* SAINTscore v. Log2(FoldChange) +Select the bubble outline color. + +**17) Crapome Filter Color** -Output.txt -- SAINTexpress "list.txt" output with additional columns that were used during the analysis - +Select color of CRAPome filtering. If *Color* is set to *crapome* this will act as the color of CRAPomePCT less than 80. If *Color* is set to *fixed* this will not be used. +