diff --git a/reports/report.Rmd b/reports/report.Rmd index 28b02fd..b55b532 100644 --- a/reports/report.Rmd +++ b/reports/report.Rmd @@ -3,6 +3,8 @@ title: "mtDNA-Server 2" output: flexdashboard::flex_dashboard: orientation: rows + navbar: + - { title: "About", href: "https://mitoverse.i-med.ac.at/#!pages/contact", align: right } params: haplogroups: ../tests/data/report/haplogroups.txt haplocheck: ../tests/data/report/haplocheck.txt @@ -10,7 +12,7 @@ params: statistics: ../tests/data/report/sample_statistics.txt mapping: ../tests/data/report/sample_mappings.txt excluded_samples: ../tests/data/report/excluded_samples.txt - pipeline_parameters: ../tests/data/report/params.txt + pipeline_parameters: ../tests/data/report/params.txt --- ```{r setup, include=FALSE} @@ -79,6 +81,8 @@ variants_count <- merge(variants_count, mapping, by.x="V2", by.y="Filename") %>% variants <- merge(variants, mapping, by.x="ID", by.y="Filename") %>% arrange(Sample_Label) +variant_caller <- pipeline_params %>% + filter(Parameter == "Variant Caller") ``` @@ -100,10 +104,10 @@ valueBox(nrow(statistics), icon = "fa-users") valueBox(nrow(excluded_samples), icon = "fa-filter") ``` -### Samples with Bad Quality +### Variant Caller ```{r} -valueBox(-1, icon = "fa-exclamation") +valueBox(paste(variant_caller$Value), icon = "fa-cog") ``` @@ -284,32 +288,3 @@ ggplotly( theme(axis.text.x=element_text(angle=+90)) ) ``` - - - ---- - -# About - -Row -------------------------------------- - -### About this report - -This software was developed at the [Institute of Genetic Epidemiology](https://genepi.i-med.ac.at/), [Medical University of Innsbruck](https://i-med.ac.at/) - -![](https://avatars2.githubusercontent.com/u/210220?s=30) [Lukas Forer](mailto:lukas.forer@i-med.ac.at) ([@lukfor](https://twitter.com/lukfor)) - -![](https://avatars2.githubusercontent.com/u/1931865?s=30) [Hansi Weissensteiner](mailto:hansi.weissensteiner@i-med.ac.at) ([@whansi](https://twitter.com/whansi)) - -![](https://avatars2.githubusercontent.com/u/1942824?s=30) [Sebastian Schoenherr](mailto:sebastian.schoenherr@i-med.ac.at) ([@seppinho](https://twitter.com/seppinho)) - -Row -------------------------------------- - -### Workflow parameters and Software versions - -```{r echo=FALSE, results='asis'} -pipeline_params %>% - kable() -```