# HG changeset patch # User bornea # Date 1463604983 14400 # Node ID ed4d14e83f445512a8decbae92dae72f217177b9 # Parent f0901a52b310c605fb781acaa8479379275e8ad5 Uploaded diff -r f0901a52b310 -r ed4d14e83f44 APOSTL_Static_Bubblegraph_Generator.xml --- a/APOSTL_Static_Bubblegraph_Generator.xml Tue May 17 13:00:42 2016 -0400 +++ b/APOSTL_Static_Bubblegraph_Generator.xml Wed May 18 16:56:23 2016 -0400 @@ -1,1429 +1,34 @@ - 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 - + 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 + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - + + + + + + - - - @@ -1435,96 +40,89 @@ -Bubble Graph Generator -^^^^^^^^^^^^^^^^^^^^^^ +Post-processing: +Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things: -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). +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: -**1) SAINT Output File** +- x axis is the natural log of the NSAF values -SAINTexpress generated *list.txt* file. +- y axis is the observed log2 fold change (as compared to control) - **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g. - "EGFR\_HUMAN" or "P00533"). +- bubble radius is proportional to the average observed spectra -**2) Prey File** +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 -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). +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. -**3) CRAPome File** +INPUTS: + +List 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. +- SAINTexpress generated "list.txt" file -**4) Interactions File** +Prey File: + +- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress -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. +Crapome File: -**5) X Axis Label** +- raw output from Crapome Workflow 1 query (http://www.crapome.org) + +Color: -Select the value to be used as the X axis in the Bubble Graph. - -**6) Y Axis Label** +- Specify the color of the bubbles within the graph. -Selct the value to be used as the Y axis in the Bubble Graph. +- If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity -**7) Bubble Size** +Use labels: -Select the value to size the bubbles in the Bubble Graph. The "fixed" -option will make all the bubbles the same size +- Adds gene name labels to bubbles within the "zoomed in" graphs +SAINT Score Cutoff: -**8) Color** +- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8) -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). +- Also used for filtering during the generation of the cytoscape network -**9) SAINT Score Cutoff** +Species: + +- Human, mouse, or yeast -SaintScore filter in range 0-1 (default 0.8) +Interaction Confidence: -**10) Fold Change Cutoff** +- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database -Fold Change filter in range -Inf to Inf (default 0) +- Suggestions: -**11) NSAF Score Cutoff** +* low: 0 -NSAF Score filter in range -Inf to Inf (default 0) +* medium: 0.5 -**12) Plot Theme** +* high: 0.7 -Select theme to be used when creating Bubble Graph. +* very high: 0.9 -**13) Label Type** +OUTPUTS: -Select the type of labeling: no labels, label points greater than CRAPomePCT cutoff, and -all bubbles labeled. +Bubble Graphs: -**14) Label Color** +- Unfiltered Data: -Select label color. +* NSAF v. Log2(FoldChange) -**15) Bubble Color** +* SAINTscore v. Log2(FoldChange) -Select color of Bubble interior. If *Color* is set to *crapome* this will act as the color of CRAPomePCT > 80. If *Color* is set to *fixed* this will be the bubble color. +- Filtered by SAINT Score -**16) Outline Color** +* NSAF v. Log2(FoldChange) -Select the bubble outline color. - -**17) Crapome Filter Color** +* SAINTscore v. Log2(FoldChange) -Select color of CRAPome filtering. If *Color* is set to *crapome* this will act as the color of CRAPomePCT < 80. If *Color* is set to *fixed* this will not be used. - +Output.txt +- SAINTexpress "list.txt" output with additional columns that were used during the analysis +