diff --git a/docs/images/screenshots/vignette/ADAR/TranscriptSet1/ADAR_5_AnchorHeatmap_TranscriptSet1.png b/docs/images/screenshots/vignette/ADAR/TranscriptSet1/ADAR_5_AnchorHeatmap_TranscriptSet1.png index dd877361..64d7422f 100644 Binary files a/docs/images/screenshots/vignette/ADAR/TranscriptSet1/ADAR_5_AnchorHeatmap_TranscriptSet1.png and b/docs/images/screenshots/vignette/ADAR/TranscriptSet1/ADAR_5_AnchorHeatmap_TranscriptSet1.png differ diff --git a/docs/images/screenshots/vignette/KIF1C-new/KIF1C_5_AnchorHeatmap.png b/docs/images/screenshots/vignette/KIF1C-new/KIF1C_5_AnchorHeatmap.png index b833081d..5721eb2e 100644 Binary files a/docs/images/screenshots/vignette/KIF1C-new/KIF1C_5_AnchorHeatmap.png and b/docs/images/screenshots/vignette/KIF1C-new/KIF1C_5_AnchorHeatmap.png differ diff --git a/docs/pvacview/pvacseq_module/pvacseq_vignette.rst b/docs/pvacview/pvacseq_module/pvacseq_vignette.rst index b8359e67..f6d1c1ca 100644 --- a/docs/pvacview/pvacseq_module/pvacseq_vignette.rst +++ b/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 previded in the ``Anchor Positions`` panel below. Additional, 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 diff --git a/pvactools/tools/pvacview/ui.R b/pvactools/tools/pvacview/ui.R index cdb5428b..59ff09d9 100644 --- a/pvactools/tools/pvacview/ui.R +++ b/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() ) )