# The `params` object is available in the document. knitr::opts_chunk$set(echo = FALSE) knitr::opts_chunk$set(warning = FALSE) knitr::opts_chunk$set(message = FALSE) params$n library(ggplot2) library(plotly) library(DT)
r params$cases
r params$controls
DT::datatable(params$patients)
if (!is.na(params$manhattan_concepts)) { cat('## UMLS concepts from narrative reports\n\n') cat('### Manhattan plot\n\n') }
if(!is.na(params$manhattan_concepts)) params$manhattan_concepts
if (!is.na(params$manhattan_concepts)) { cat('### Result table\n\n') }
if(!is.na(params$table_concepts)) DT::datatable(params$table_concepts)
if (!is.na(params$dumbbell_concepts)) { cat('### Dumbbell plot of bootstrapped ORs\n\n') }
if(!is.na(params$dumbbell_concepts)) params$dumbbell_concepts
if (!is.na(params$dumbbell_concepts)) { cat('### Dumbbell plot of bootstrapped ORs\n\n') }
if(!is.na(params$dumbbell_concepts)) params$dumbbell_concepts
if (!is.na(params$manhattan_bio)) { cat('## Biological test results\n\n') cat('### Manhattan plot\n\n') }
if(!is.na(params$manhattan_bio)) params$manhattan_bio
if (!is.na(params$table_bio)) { cat('### Result table\n\n') }
if(!is.na(params$table_bio)) DT::datatable(params$table_bio)
if (!is.na(params$dumbbell_bio)) { cat('### Dumbbell plot of bootstrapped ORs\n\n') }
if(!is.na(params$dumbbell_bio)) params$dumbbell_bio
if (!is.na(params$manhattan_cim)) { cat('## ICD codes\n\n') cat('### Manhattan plot\n\n') }
if(!is.na(params$manhattan_cim)) params$manhattan_cim
if (!is.na(params$table_cim)) { cat('### Result table\n\n') }
if(!is.na(params$table_cim)) DT::datatable(params$table_cim)
if (!is.na(params$dumbbell_cim)) { cat('### Dumbbell plot of bootstrapped ORs\n\n') }
if(!is.na(params$dumbbell_cim)) params$dumbbell_cim
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