cosmetic fixes

sigven · Feb 24, 2025 · 048c6c1 · 048c6c1
1 parent 94d2e48
commit 048c6c1
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Showing 5 changed files with 16 additions and 36 deletions.
diff --git a/R/classification.R b/R/classification.R
@@ -874,7 +874,8 @@ assign_pathogenicity_evidence <- function(var_calls, settings, ref_data) {
         as.character(NA)
       )
     ) |>
-    tidyr::separate("HGVSp",c("tmpENSP","HGVSp_long"),sep=":") |>
+    tidyr::separate(
+      "HGVSp",c("tmpENSP","HGVSp_long"),sep=":", remove = F) |>
     dplyr::left_join(
       essential_nucleotides,
       by = c("ENTREZGENE", "NUC_SITE")
@@ -893,6 +894,12 @@ assign_pathogenicity_evidence <- function(var_calls, settings, ref_data) {
     dplyr::left_join(
       benign_codons,
       by = c("ENTREZGENE","CODON")) |>
+    dplyr::rename(
+      "HGVSp_short" = "HGVSP"
+    ) |>
+    dplyr::select(
+      -c("HGVSp_long","tmpENSP")
+    ) |>
 
     ## at same codon, but not the same variant (VAR_ID)
     dplyr::mutate(ACMG_PM5 = dplyr::if_else(

diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R
@@ -218,7 +218,6 @@ col_format_output[['tsv']] <-
     "CPSR_CLASSIFICATION",
     "CPSR_PATHOGENICITY_SCORE",
     "CPSR_CLASSIFICATION_CODE",
-    "CPSR_CLASSIFICATION_DOC",
     "CPSR_CLASSIFICATION_SOURCE"
   )
 

diff --git a/data/col_format_output.rda b/data/col_format_output.rda
diff --git a/inst/templates/cpsr.css b/inst/templates/cpsr.css
@@ -1,6 +1,6 @@
 
 h1.title {
-  font-size: 34px;
+  font-size: 30px;
   color: black;
 }
 
@@ -16,6 +16,12 @@ h2, #TOC>ul>li {
   color: black;
 }
 
+.quarto-title-banner {
+  /*height: 120px;*/
+  margin-left: -15px;
+  margin-right: -15px;
+  margin-top: 0px;
+}
 
 #container {
     /*border: 2px dashed #444;*/
@@ -126,40 +132,9 @@ h2, #TOC>ul>li {
   color: white;
 }
 
-
-.panel-tabset > .nav-tabs > .nav-item > .nav-link{
-  color: #007a74;
-}
-
-.tabset-margin-container{
-  color: white;
-  background-color: #007a74;
-}
-/*
-.sidebar .margin-sidebar .toc-active .nav-link a {
-  color: #007a74
-}
-*/
-
 .sidebar nav[role="doc-toc"] ul > li > a.active a.hover {
     color: #007a74 !important;
 }
 
-/*
-.quarto-title-block .quarto-title-banner {
-  /*background-image: url(../../man/figures/logo.png);
-  background-size: 150px;
-  background-position: left;
-  background-repeat: no-repeat;
-  padding-left: 10px;
-  background-origin: content-box;
-}
-*/
 
-/*
-.nav .navbar li.nav-item a.nav-link span {
-  color: #007a74 !important;
-  background-color: #007a74 !important;
-}
-*/
 
diff --git a/inst/templates/cpsr_report.qmd b/inst/templates/cpsr_report.qmd
@@ -27,7 +27,7 @@ format:
     fontsize: 0.93em
     toc: true
     toc-depth: 3
-    toc-expqand: 3
+    toc-expand: 3
     toc-title: Contents
     grid:
       body-width: 940px
@@ -83,7 +83,6 @@ cat("</ul><br>")
 #| eval: !expr as.logical(cps_report$content$snv_indel$eval)
 ```
 
-<br>
 
 ```{r biomarkers_cpsr} 
 #| child: 'quarto/cpsr_biomarkers.qmd'