Added new PSM vs/ Q-value QC plot to documentation.

yeastrc · Nov 6, 2015 · a857d13 · a857d13
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diff --git a/docs/images/project-overview-explore-data2.png b/docs/images/project-overview-explore-data2.png
diff --git a/docs/images/project-overview-psm-count-over-qvalue-qc.png b/docs/images/project-overview-psm-count-over-qvalue-qc.png
diff --git a/docs/using/project.rst b/docs/using/project.rst
@@ -184,7 +184,7 @@ Search information includes the following information for each search:
 
 Retention Time QC Plot
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Clicking the "Retention Time" link next to "QC Plots:" produces the retention time QC plot:
+Clicking the "[Retention Time]" link next to "QC Plots:" produces the retention time QC plot:
 
 .. image:: /images/project-overview-rt.png
 
@@ -199,6 +199,25 @@ The chart options are:
 	* Scans with - Counts for "Filtered PSMs" will only include scans that resulted in a PSM where the peptide was of a type that is checked here. E.g., if only "crosslinks" is checked, only scans that resulted in crosslinked peptides will be used to for "Fitlered PSMs" counts. If "looplinks" and "crosslinks" are checked, only PSMs resulting in crosslinked or looplinked peptides will be counted.
 	* Max - Values entered here will be the maximum value on the X or Y axis--used for rescaling the chart.
 
+Cumulative PSM Count vs/ Q-value QC Plot
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Clicking the "[PSM Q Values]" link next to "QC Plots:" produces a plot of cumulative PSM count vs/ q-value cutoff:
+
+.. image:: /images/project-overview-psm-count-over-qvalue-qc.png
+
+Q-value cutoff is presented on the x-axis, and y-values are the total number of PSMs found in this search with that q-value or lower. Each class
+of PSM is presented as a separate line: crosslinks, looplinks, and unlinked. A line for all PSM types combined may optionally be displayed by checking "all"
+in the "PSMs with:" options. 
+
+The "View as:" option allows switching between raw counts (default) and percentage. The "raw counts" option uses the raw PSM counts for the respective types.
+The percentage option displays the PSM counts as the percentage the total PSMs of the respective type, and so applies the same scale to all lines, which will
+always move from 0 to 100 in the plot.
+
+The "PSMs with:" options toggle the visibility of the lines corresponding to the respective class of PSM.
+
+The "Max:" options allow for a user-supplied maximum for the X- and Y-axes. "Reset" clears the user-supplied maximum values.
+
+
 View Data
 --------------------------------
 .. image:: /images/project-overview-explore-data3.png