# HG changeset patch
# User bornea
# Date 1463504442 14400
# Node ID f0901a52b310c605fb781acaa8479379275e8ad5
# Parent  4f032e16df3a1e014a66e523ed48f8c9fcfcb428
Uploaded

diff -r 4f032e16df3a -r f0901a52b310 APOSTL_Static_Bubblegraph_Generator.xml
--- a/APOSTL_Static_Bubblegraph_Generator.xml	Wed May 11 15:12:27 2016 -0400
+++ b/APOSTL_Static_Bubblegraph_Generator.xml	Tue May 17 13:00:42 2016 -0400
@@ -1438,7 +1438,7 @@
 Bubble Graph Generator
 ^^^^^^^^^^^^^^^^^^^^^^
 
-This Bubble Graph Generator is static version of the APOSTL interactive affinity proteomics analysis 
+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). 
@@ -1456,11 +1456,11 @@
 
 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.
+length, and prey gene name (no header).
 
 **3) CRAPome File**
 
-Please specify an *CRAPome* file for Bubble Graph creation. An *Inter*
+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.
 
@@ -1473,7 +1473,7 @@
 
 **5) X Axis Label**
 
-Selct the value to be used as the X axis in the Bubble Graph.
+Select the value to be used as the X axis in the Bubble Graph.
 
 **6) Y Axis Label**
 
@@ -1481,9 +1481,8 @@
 
 **7) Bubble Size**
 
-Selct the value to size the bubbles in the Bubble Graph. The "fixed"
-option will make all the bubbles the same size (must be used if no-crapome 
-file is provided).
+Select the value to size the bubbles in the Bubble Graph. The "fixed"
+option will make all the bubbles the same size
 
 **8) Color**
 
@@ -1509,7 +1508,7 @@
 
 **13) Label Type**
 
-Select the type of labeling, no labels, lable those greater than cutoff, and 
+Select the type of labeling: no labels, label points greater than CRAPomePCT cutoff, and 
 all bubbles labeled.
 
 **14) Label Color**
@@ -1518,8 +1517,7 @@
 
 **15) Bubble Color**
 
-Select color of Bubble interior. If *8* is set to crapome this will act as the good 
-crapome score. If *8* is set to fixed this will be the bubble color.
+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.
 
 **16) Outline Color**
 
@@ -1527,7 +1525,6 @@
 
 **17) Crapome Filter Color**
 
-Select color of crapome filtering. If *8* is set to crapome this will act as the poor 
-crapome score. If *8* is set to fixed this will not be used.
+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.
     </help>
 </tool>