update ClinVar concordance plot

sigven · Mar 11, 2024 · fe7edb8 · fe7edb8
1 parent 232d8f8
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Showing 3 changed files with 10 additions and 9 deletions.
diff --git a/inst/extdata/CPSR_classification_score_thresholds.png b/inst/extdata/CPSR_classification_score_thresholds.png
diff --git a/inst/templates/quarto/cpsr_documentation.qmd b/inst/templates/quarto/cpsr_documentation.qmd
@@ -104,7 +104,7 @@ classification_calibration_plot_fname_path <-
               package = "cpsr")
 ```
 
-<img src="`r classification_calibration_plot_fname_path`" title="" alt="" align="center" width="950" height="530"/>
+<img src="`r classification_calibration_plot_fname_path`" title="" alt="" align="center" width="950" height="560"/>
 
 <br>
 <br>

diff --git a/inst/templates/quarto/cpsr_virtual_panel.qmd b/inst/templates/quarto/cpsr_virtual_panel.qmd
@@ -5,13 +5,6 @@
 Variants reported for the sample are limited to the tile of cancer predisposition genes
 shown below. 
 
-::: {.callout-note}
-CPSR does not perform any interrogation of _which genes 
-that were subject to sequencing_, it merely checks potential overlap of input variants 
-within the user-defined __virtual__ panel.
-:::
-
-
    *  __`r cps_report[['settings']][['conf']][['gene_panel']][['description']]`__
       * Diagnostic-grade genes only (applicable to Genomics England panels): __`r as.logical(cps_report[['settings']][['conf']][['gene_panel']][['diagnostic_grade_only']])`__
 
@@ -22,4 +15,12 @@ tiles_html <- cpsr::plot_virtual_panels(
 
 `r tiles_html`
 
-<br><br>
+<br>
+
+::: {.callout-note}
+CPSR does not perform any interrogation of _which genes 
+that were subject to sequencing_, it merely checks potential overlap of input variants 
+within the user-defined __virtual__ gene panel.
+:::
+
+<br>