dark color update

sigven · Mar 26, 2024 · 7ca2e6b · 7ca2e6b
1 parent 4715e03
commit 7ca2e6b
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Showing 5 changed files with 124 additions and 52 deletions.
diff --git a/inst/templates/cpsr.css b/inst/templates/cpsr.css
@@ -49,7 +49,7 @@ h2, #TOC>ul>li {
 */
 
 .exploratory {
-  background: #000;
+  background: #2c313c;
   border-radius: 5px;
 
 }
@@ -88,7 +88,7 @@ h2, #TOC>ul>li {
 
 .custom {
   /*background: darkmagenta;*/
-  background: #000;
+  background: #2c313c;
   border-radius: 5px;
 
 }

diff --git a/inst/templates/cpsr_report.qmd b/inst/templates/cpsr_report.qmd
@@ -23,11 +23,11 @@ format:
     embed-resources: true
     smooth-scroll: true
     page-layout: full
-    fontsize: 0.9em
+    fontsize: 0.92em
     toc: true
     toc_depth: 2
     grid:
-      body-width: 920px
+      body-width: 940px
 css: cpsr.css
 
 ---
@@ -106,12 +106,15 @@ options(scipen = 0)
 
 <br><br>
 
+<font size="-1">
 
 ## References
 
 ::: {#refs}
 :::
 
+</font>
+
 ```{r cpsr_disclaimer}
 #| eval: true
 #| output: asis

diff --git a/inst/templates/quarto/cpsr_biomarkers.qmd b/inst/templates/quarto/cpsr_biomarkers.qmd
@@ -11,7 +11,8 @@ missing_germline_items <- list()
 biomarker_present <- F
 etype_set <- list()
 
-for (etype in c("Predictive","Diagnostic","Predisposing","Prognostic")) {
+for (etype in c("Predictive","Diagnostic",
+                "Predisposing","Prognostic")) {
   show_germline_filters[[tolower(etype)]] <- F
   missing_germline_items[[tolower(etype)]] <- T
   
@@ -61,7 +62,9 @@ As indicated from the variant-association numbers above, the same germline mutat
 
 cat("\n::: {.callout-note}\n## Note - biomarker resolution\n\n Biomarkers registered in CIViC/CGI are provided at different _resolutions_ (i.e. filter <b>Biomarker resolution</b>). The accuracy of a match between a variant in the sample and a clinical evidence item (biomarker) will vary accordingly (highlighted by gene symbols with different color backgrounds):\n\n")
 
-cat('<ul><li>Biomarker match at the <mark style="background-color:black; font-weight:bold; color:white">&nbsp; genomic position/amino acid/codon level &nbsp;</mark></li>')
+cat('<ul><li>Biomarker match at the <mark style="background-color:',
+    pcgrr::color_palette$bg_dark,
+    '; font-weight:bold; color:white">&nbsp; genomic position/amino acid/codon level&nbsp;</mark></li>')
 cat(paste0('<br><li>Biomarker match at the <mark style="background-color:', 
            pcgrr::color_palette$warning,
            '; color:white; font-weight:bold">&nbsp; exon/gene level&nbsp; </mark></li></ul>\n\n:::'))
@@ -102,13 +105,23 @@ variants_germline_predisposing_shared <- crosstalk::SharedData$new(
   etype_set[['predisposing']])
 crosstalk::bscols(
   list(
-    crosstalk::filter_select("BM_CANCER_TYPE", "Cancer type", variants_germline_predisposing_shared, ~BM_CANCER_TYPE),
-    crosstalk::filter_select("BM_CLINICAL_SIGNIFICANCE", "Clinical significance", variants_germline_predisposing_shared, ~BM_CLINICAL_SIGNIFICANCE),
-    crosstalk::filter_select("BM_EVIDENCE_LEVEL", "Evidence level", variants_germline_predisposing_shared, ~BM_EVIDENCE_LEVEL)
+    crosstalk::filter_select(
+      "BM_CANCER_TYPE", "Cancer type", 
+      variants_germline_predisposing_shared, ~BM_CANCER_TYPE),
+    crosstalk::filter_select(
+      "BM_CLINICAL_SIGNIFICANCE", "Clinical significance",
+      variants_germline_predisposing_shared, ~BM_CLINICAL_SIGNIFICANCE),
+    crosstalk::filter_select(
+      "BM_EVIDENCE_LEVEL", "Evidence level", 
+      variants_germline_predisposing_shared, ~BM_EVIDENCE_LEVEL)
   ),
   list(
-    crosstalk::filter_select("SYMBOL", "Gene", variants_germline_predisposing_shared, ~SYMBOL),
-    crosstalk::filter_select("BM_RESOLUTION", "Biomarker resolution", variants_germline_predisposing_shared, ~BM_RESOLUTION)
+    crosstalk::filter_select(
+      "SYMBOL", "Gene", 
+      variants_germline_predisposing_shared, ~SYMBOL),
+    crosstalk::filter_select(
+      "BM_RESOLUTION", "Biomarker resolution", 
+      variants_germline_predisposing_shared, ~BM_RESOLUTION)
   )
 )
 
@@ -137,11 +150,16 @@ DT::datatable(variants_germline_predisposing_shared,
     fontWeight = "bold", 
     `text-align` = "center",
     backgroundColor = DT::styleEqual(
-      c("genomic", "hgvsp", "codon", 
-        "hgvsp_nonprincipal", "exon", "gene"),
-      c("#000", "#000", "#000","#000",
-        pcgrr::color_palette$warning,
-        pcgrr::color_palette$warning)
+      c('genomic','hgvsp','codon',
+        'exon','gene_region_mut',
+        'gene_lof','gene_mut'), 
+      c(pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']])
     )
   )
 ```
@@ -186,15 +204,26 @@ variants_germline_predictive_shared <- crosstalk::SharedData$new(
   etype_set[['predictive']])
 crosstalk::bscols(
   list(
-    crosstalk::filter_select("BM_CANCER_TYPE", "Cancer type", variants_germline_predictive_shared, ~BM_CANCER_TYPE),
-    crosstalk::filter_select("BM_CLINICAL_SIGNIFICANCE", "Clinical significance", variants_germline_predictive_shared, ~BM_CLINICAL_SIGNIFICANCE),
-    crosstalk::filter_select("BM_EVIDENCE_LEVEL", "Evidence level", variants_germline_predictive_shared, ~BM_EVIDENCE_LEVEL)
+    crosstalk::filter_select(
+      "BM_CANCER_TYPE", "Cancer type", 
+      variants_germline_predictive_shared, ~BM_CANCER_TYPE),
+    crosstalk::filter_select(
+      "BM_CLINICAL_SIGNIFICANCE", "Clinical significance", 
+      variants_germline_predictive_shared, ~BM_CLINICAL_SIGNIFICANCE),
+    crosstalk::filter_select(
+      "BM_EVIDENCE_LEVEL", "Evidence level", 
+      variants_germline_predictive_shared, ~BM_EVIDENCE_LEVEL)
   ),
   list(
-    crosstalk::filter_select("SYMBOL", "Gene", variants_germline_predictive_shared, ~SYMBOL),
-    crosstalk::filter_select("BM_RESOLUTION", "Biomarker resolution", 
-                             variants_germline_predictive_shared, ~BM_RESOLUTION),
-    crosstalk::filter_select("BM_THERAPEUTIC_CONTEXT", "Therapeutic context", variants_germline_predictive_shared, ~BM_THERAPEUTIC_CONTEXT)
+    crosstalk::filter_select(
+      "SYMBOL", "Gene", 
+      variants_germline_predictive_shared, ~SYMBOL),
+    crosstalk::filter_select(
+      "BM_RESOLUTION", "Biomarker resolution", 
+      variants_germline_predictive_shared, ~BM_RESOLUTION),
+    crosstalk::filter_select(
+      "BM_THERAPEUTIC_CONTEXT", "Therapeutic context", 
+      variants_germline_predictive_shared, ~BM_THERAPEUTIC_CONTEXT)
   )
 )
 
@@ -222,11 +251,16 @@ DT::datatable(
     fontWeight = "bold", 
     `text-align` = "center",
     backgroundColor = DT::styleEqual(
-      c("genomic", "hgvsp", "codon", 
-        "hgvsp_nonprincipal", "exon", "gene"),
-      c("#000", "#000", "#000","#000",
-        pcgrr::color_palette$warning,
-        pcgrr::color_palette$warning)
+      c('genomic','hgvsp','codon',
+        'exon','gene_region_mut',
+        'gene_lof','gene_mut'), 
+      c(pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']])
     )
   )
 ```
@@ -272,22 +306,36 @@ variants_germline_prognostic_shared <- crosstalk::SharedData$new(
   etype_set[['prognostic']])
 crosstalk::bscols(
   list(
-    crosstalk::filter_select("SYMBOL", "Gene", variants_germline_prognostic_shared, ~SYMBOL),
-    crosstalk::filter_select("BM_CANCER_TYPE", "Cancer type", variants_germline_prognostic_shared, ~BM_CANCER_TYPE),
-    crosstalk::filter_select("BM_CLINICAL_SIGNIFICANCE", "Clinical significance", variants_germline_prognostic_shared, ~BM_CLINICAL_SIGNIFICANCE)
+    crosstalk::filter_select(
+      "SYMBOL", "Gene", 
+      variants_germline_prognostic_shared, ~SYMBOL),
+    crosstalk::filter_select(
+      "BM_CANCER_TYPE", "Cancer type", 
+      variants_germline_prognostic_shared, ~BM_CANCER_TYPE),
+    crosstalk::filter_select(
+      "BM_CLINICAL_SIGNIFICANCE", "Clinical significance", 
+      variants_germline_prognostic_shared, ~BM_CLINICAL_SIGNIFICANCE)
   ),
   list(
-    crosstalk::filter_select("BM_EVIDENCE_LEVEL", "Evidence level", variants_germline_prognostic_shared, ~BM_EVIDENCE_LEVEL),
-    crosstalk::filter_select("BM_RESOLUTION", "Biomarker resolution", variants_germline_prognostic_shared, ~BM_RESOLUTION)
+    crosstalk::filter_select(
+      "BM_EVIDENCE_LEVEL", "Evidence level", 
+      variants_germline_prognostic_shared, ~BM_EVIDENCE_LEVEL),
+    crosstalk::filter_select(
+      "BM_RESOLUTION", "Biomarker resolution", 
+      variants_germline_prognostic_shared, ~BM_RESOLUTION)
   )
 )
 ##cat("The table below lists all variant-evidence item associations:", sep = "\n")
 htmltools::br()
 htmltools::br()
 
-DT::datatable(variants_germline_prognostic_shared, escape = F, extensions = c("Buttons", "Responsive"), options = list(
-  buttons = c("csv", "excel"),
-  pageLength = 6, dom = "Bfrtip")) |>
+DT::datatable(
+  variants_germline_prognostic_shared, 
+  escape = F, 
+  extensions = c("Buttons", "Responsive"), 
+  options = list(
+    buttons = c("csv", "excel"),
+    pageLength = 6, dom = "Bfrtip")) |>
    DT::formatStyle("BM_EVIDENCE_LEVEL",
     backgroundColor = DT::styleEqual(
       pcgrr::color_palette$clinical_evidence$levels,
@@ -301,10 +349,16 @@ DT::datatable(variants_germline_prognostic_shared, escape = F, extensions = c("B
     fontWeight = "bold", 
     `text-align` = "center",
     backgroundColor = DT::styleEqual(
-      c("genomic", "hgvsp", "codon", "hgvsp_nonprincipal", "exon", "gene"),
-      c("#000", "#000", "#000","#000",
-        pcgrr::color_palette$warning,
-        pcgrr::color_palette$warning)
+      c('genomic','hgvsp','codon',
+        'exon','gene_region_mut',
+        'gene_lof','gene_mut'), 
+      c(pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']])
     )
   )
 ```
@@ -350,13 +404,23 @@ variants_germline_diagnostic_shared <- crosstalk::SharedData$new(
   etype_set[['diagnostic']])
 crosstalk::bscols(
   list(
-    crosstalk::filter_select("SYMBOL", "Gene", variants_germline_diagnostic_shared, ~SYMBOL),
-    crosstalk::filter_select("BM_CANCER_TYPE", "Cancer type", variants_germline_diagnostic_shared, ~BM_CANCER_TYPE),
-    crosstalk::filter_select("BM_CLINICAL_SIGNIFICANCE", "Clinical association", variants_germline_diagnostic_shared, ~BM_CLINICAL_SIGNIFICANCE)
+    crosstalk::filter_select(
+      "SYMBOL", "Gene", 
+      variants_germline_diagnostic_shared, ~SYMBOL),
+    crosstalk::filter_select(
+      "BM_CANCER_TYPE", "Cancer type", 
+      variants_germline_diagnostic_shared, ~BM_CANCER_TYPE),
+    crosstalk::filter_select(
+      "BM_CLINICAL_SIGNIFICANCE", "Clinical association", 
+      variants_germline_diagnostic_shared, ~BM_CLINICAL_SIGNIFICANCE)
   ),
   list(
-    crosstalk::filter_select("BM_EVIDENCE_LEVEL", "Evidence level", variants_germline_diagnostic_shared, ~BM_EVIDENCE_LEVEL),
-    crosstalk::filter_select("BM_RESOLUTION", "Biomarker resolution", variants_germline_diagnostic_shared, ~BM_RESOLUTION)
+    crosstalk::filter_select(
+      "BM_EVIDENCE_LEVEL", "Evidence level", 
+      variants_germline_diagnostic_shared, ~BM_EVIDENCE_LEVEL),
+    crosstalk::filter_select(
+      "BM_RESOLUTION", "Biomarker resolution", 
+      variants_germline_diagnostic_shared, ~BM_RESOLUTION)
   )
 )
 ##cat("The table below lists all variant-evidence item associations:", sep = "\n")
@@ -382,11 +446,16 @@ DT::datatable(variants_germline_diagnostic_shared,
     fontWeight = "bold", 
     `text-align` = "center",
     backgroundColor = DT::styleEqual(
-      c("genomic", "hgvsp", "codon", 
-        "hgvsp_nonprincipal", "exon", "gene"),
-      c("#000", "#000", "#000","#000",
-        pcgrr::color_palette$warning,
-        pcgrr::color_palette$warning)
+      c('genomic','hgvsp','codon',
+        'exon','gene_region_mut',
+        'gene_lof','gene_mut'), 
+      c(pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette$bg_dark,
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']],
+        pcgrr::color_palette[['warning']])
     )
   )
 ```

diff --git a/inst/templates/quarto/cpsr_classification.qmd b/inst/templates/quarto/cpsr_classification.qmd
@@ -530,7 +530,7 @@ DT::datatable(variants_class3_1,
     dom = "Bfrtip",
     initComplete = DT::JS(
       "function(settings, json) {",
-      "$(this.api().table().header()).css({'background-color':'#000000', 'color': '#fff'});",
+      "$(this.api().table().header()).css({'background-color':'#2c313c', 'color': '#fff'});",
       "}"
     )
   )

diff --git a/inst/templates/quarto/cpsr_summary.qmd b/inst/templates/quarto/cpsr_summary.qmd
@@ -12,7 +12,7 @@ color_report <- "#007a74"
 
 color_clinvar <- color_report
 color_novel <- color_report
-color_vus <- "#000"
+color_vus <- "#2c313c"
 
 n_clinvar <- cps_report$content$snv_indel$callset$variant_display$cpg_non_sf |>
   dplyr::filter(.data$CPSR_CLASSIFICATION_SOURCE == "ClinVar") |>