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Add design to report #189

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merged 5 commits into from
Nov 22, 2023
Merged

Add design to report #189

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1887890
Add DESeq2 designs to report
WackerO Nov 8, 2023
1babd7d
Merge branch 'dev' of https://github.com/nf-core/differentialabundanc…
WackerO Nov 21, 2023
ea326ae
Model is now added to report from the model output files
WackerO Nov 21, 2023
b86fbdc
Made deseq script like the one in dev
WackerO Nov 21, 2023
8d5ea35
Update changelog
WackerO Nov 21, 2023
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15 changes: 14 additions & 1 deletion assets/differentialabundance_report.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -438,6 +438,19 @@ Comparisons were made between `r params$observations_type` groups defined using
```{r, echo=FALSE, results='asis'}
contrasts_to_print <- contrasts
colnames(contrasts_to_print) <- prettifyVariablename(colnames(contrasts_to_print))

# Add design/model formulae to report
de_tool <- ifelse(params$study_type %in% c('rnaseq'), "deseq2", "limma")
contrasts_to_print$model <- sapply(contrasts_to_print$Id, function(id) {
model_file <- paste0(id, ".", de_tool, ".model.txt")
if (file.exists(model_file)) {
first_line <- readLines(model_file, n = 1)
return(first_line)
} else {
return(NA)
}
})

print( htmltools::tagList(datatable(contrasts_to_print, caption = paste0("Table of contrasts"), rownames = FALSE, options = list(dom = 't')) ))
```

Expand Down Expand Up @@ -944,4 +957,4 @@ print( htmltools::tagList(datatable(versions_table, caption = "Software versions

```{r, echo=FALSE, results='asis'}
htmltools::includeMarkdown(params$citations)
```
```
4 changes: 3 additions & 1 deletion workflows/differentialabundance.nf
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Expand Up @@ -342,6 +342,7 @@ workflow DIFFERENTIALABUNDANCE {
ch_samples_and_matrix
)
ch_differential = LIMMA_DIFFERENTIAL.out.results
ch_model = LIMMA_DIFFERENTIAL.out.model

ch_versions = ch_versions
.mix(LIMMA_DIFFERENTIAL.out.versions)
Expand Down Expand Up @@ -376,6 +377,7 @@ workflow DIFFERENTIALABUNDANCE {

ch_norm = DESEQ2_NORM.out.normalised_counts
ch_differential = DESEQ2_DIFFERENTIAL.out.results
ch_model = DESEQ2_DIFFERENTIAL.out.model

ch_versions = ch_versions
.mix(DESEQ2_DIFFERENTIAL.out.versions)
Expand Down Expand Up @@ -517,6 +519,7 @@ workflow DIFFERENTIALABUNDANCE {
.combine(ch_css_file)
.combine(ch_citations_file)
.combine(ch_differential.map{it[1]}.toList())
.combine(ch_model.map{it[1]}.toList())

if (params.gsea_run){
ch_report_input_files = ch_report_input_files
Expand Down Expand Up @@ -574,7 +577,6 @@ workflow DIFFERENTIALABUNDANCE {
}

// Render the final report

RMARKDOWNNOTEBOOK(
ch_report_file,
ch_report_params,
Expand Down