finally fixed logo; also re-added colorbar to sample metadata

WackerO · Jun 17, 2024 · b886173 · b886173
1 parent 8559abf
commit b886173
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd
@@ -52,6 +52,7 @@ params:
     path_quote: ''
     path_software_versions: ''
     revision: ''
+    logo: ''
 
     #Additional arg to indicate that a github test is run
     citest: ''
@@ -301,7 +302,12 @@ author: "`r PM`, Bioinformatics Research Scientist"
 date: '`r format(Sys.Date(), "%B %d, %Y")`'
 ---
 
-<img src="./logo.png" style="position:absolute;top:0px;right:0px;" height="200" width="200" />
+```{r logo, echo=FALSE, results='asis'}
+logo_file = file.path(getwd(), "logo.png")
+img_data <- base64enc::dataURI(file = logo_file, mime = "image/png") # Need to use base64 because the logo will otherwise for some reason not be loaded correctly
+cat(sprintf('<img src="%s" style="position:absolute;top:0px;right:0px;" height="200" width="200" />', img_data))
+```
+
 <div class="watermark">QBiC</div>
 
 ```{r docSetup, bootstrap.show.code = FALSE, dev = c('png'), bootstrap.show.message=FALSE, echo=FALSE, message=FALSE, warning=FALSE}
@@ -1027,7 +1033,7 @@ if (mqc_version == 'old_mqc') {
     table_complete <- table_complete %>%
         mutate(
             Sample = Sample,
-            ReadNumber = round((ReadNumber/1000000),2),
+            ReadNumber = color_bar("lightblue")(round((ReadNumber/1000000),2)),
             DuplicateReadsIntercept = ifelse(DuplicateReadsIntercept > 1,
                                             cell_spec(DuplicateReadsIntercept, color="orange", bold=T),
                                             cell_spec(DuplicateReadsIntercept, color="black")),

diff --git a/bin/Execute_report.R b/bin/Execute_report.R
@@ -42,6 +42,7 @@ option_list = list(
     make_option(c("--path_quote"), type="character", default=NULL, help="Path to the quote PDF", metavar="character"),
     make_option(c("-v", "--software_versions"), type="character", default=NULL, help="Versions file", metavar="character"),
     make_option(c("-j", "--revision"), type="character", default=NULL, help="Rnadeseq workflow revision", metavar="character"),
+    make_option("--logo", type="character", default=NULL, help="Logo image file", metavar="character"),
 
     make_option("--citest", action="store_true", default=FALSE, help="Run github test and don't save pathway heatmaps.")
 )
@@ -93,5 +94,6 @@ rmarkdown::render(opt$report, output_file = opt$output, knit_root_dir = wd, outp
                                 path_quote = opt$path_quote,
                                 path_software_versions = opt$software_versions,
                                 revision = opt$revision,
+                                logo = opt$logo,
 
                                 citest = opt$citest))
diff --git a/modules/local/report.nf b/modules/local/report.nf
@@ -91,6 +91,7 @@ process REPORT {
         $software_versions_opt \
         --proj_summary $proj_summary \
         --revision $workflow.manifest.version \
+        --logo $logo \
         $citest_opt
 
     # Remove allgenes dir as the contained files do not contain only DE genes