Merge pull request #1144 from griffithlab/pvacview_anchor

Update pVACview anchor figure

docs/pvacview/pvacseq_module/pvacseq_vignette.rst

@@ -219,7 +219,11 @@ The candidate being investigated has a good binding affinity (median IC50 score
     :alt: pVACview Vignette
     :figclass: align-left
 
-The mutation is not in an anchor position (see ``Anchor heatmap`` tab). Anchor prediction scores for each amino acid position are provided in the ``Anchor Weights`` tab at the bottom. Both mutant and wildtype peptides are good binders, yet the mutant peptide is a stronger binder. This is scenario number 2 (WT strong binder, MT strong binder, MT not in an anchor position) according to the Scenario Guide, where the neoantigen candidate is favorable and can be accepted.
+The mutation is not in an anchor position (see ``Anchor heatmap`` tab). A list of anchor positions for each allele-length combination
+is provided in the ``Anchor Positions`` panel below. Additionally, the underlying anchor prediction scores for each amino acid position are
+provided in the ``Anchor Weights`` panel at the bottom. Both mutant and wildtype peptides are good binders, yet the mutant peptide
+is a stronger binder. This is scenario number 2 (WT strong binder, MT strong binder, MT not in an anchor position) according to the Scenario
+Guide, where the neoantigen candidate is favorable and can be accepted.
 
 .. figure:: ../../images/screenshots/vignette/KIF1C-new/KIF1C_5_AnchorHeatmap.png
     :width: 1000px
@@ -330,7 +334,9 @@ The candidate also has good elution scores (elution scores close to 1). It's unc
     :alt: pVACview Vignette
     :figclass: align-left
 
-Altogether, both the candidate (mutant peptide - MT) and its wildtype (WT) peptide are strong binders. The figure below shows the mutated amino acid (V) in the candidate is not in an anchor position. This fits into Scenario 4 in the guide, where the candidate is likely to elicit strong recognition from the immune system.
+Altogether, both the candidate (mutant peptide - MT) and its wildtype (WT) peptide are strong binders. The figure below shows the mutated
+amino acid (V) in the candidate (AERMGFTVV) is not in an anchor position for allele HLA-B*45:01. This fits into Scenario 4 in the guide,
+where the candidate is likely to elicit strong recognition from the immune system.
 
 .. figure:: ../../images/screenshots/vignette/ADAR/TranscriptSet1/ADAR_5_AnchorHeatmap_TranscriptSet1.png
     :width: 1000px

pvactools/tools/pvacview/ui.R

@@ -233,7 +233,7 @@ explore_tab <- tabItem(
                             ) %>% withSpinner(color = "#8FCCFA"), style = "overflow-x: scroll; overflow-y: scroll",
                             column(width = 6,
                                    h4("Anchor vs Mutation position Scenario Guide",
-                                      img(src = "https://github.com/griffithlab/pVACtools/raw/5834def4/pvactools/tools/pvacview/www/anchor.jpg",
+                                      img(src = "https://github.com/griffithlab/pVACtools/raw/f19788ccdb313a14a57350557cd70e1aa6bdca9a/pvactools/tools/pvacview/www/anchor.jpg",
                                           align = "center", width = "100%")
                                    )
                             )
@@ -579,7 +579,7 @@ tutorial_tab <- tabItem("tutorial",
                 p(strong("Scenario 4 : "), code(" I + III"), strong(" -> Accept"))
             ),
             column(width = 6,
-                img(src = "https://github.com/griffithlab/pVACtools/raw/5834def4/pvactools/tools/pvacview/www/anchor.jpg",
+                img(src = "https://github.com/griffithlab/pVACtools/raw/f19788ccdb313a14a57350557cd70e1aa6bdca9a/pvactools/tools/pvacview/www/anchor.jpg",
                     align = "center", height = "350px", width = "600px"), br(), br()
             )
         )