---
title: "CALANGO Report"
---
<img src="https://raw.githubusercontent.com/fcampelo/CALANGO/8e2c9efd7abb739f91a2ff36ffbce2b30f98f87b/inst/images/CALANGO_LOGO.svg" alt="CALANGO logo. Drawn by Brazilian artist Berze - https://www.facebook.com/berzearte" height="300"/>

*****

CALANGO is an annotation-based comparative genomics tool that searches for annotation terms, as defined in controlled dictionaries, associated with a quantitative phenotype across phenotypes.

CALANGO provides three main outputs as interactive HTML5 files:

- Heatmaps

- Scatterplots of q-values of annotation terms

- Table of annotation terms and their statistics

To access these interactive visualizations please click on the `Results` button in the top bar.

***

## Input configuration used
The current report was generated based on the input parameters listed below.

Job finished at: `r Sys.time()`
```{r, echo = FALSE}
defs2 <- restore_relative_paths(defs)
confs <- defs2[c("annotation.files.dir", 
                 "output.dir",
                 "dataset.info",
                 "x.column",
                 "short.name.column",
                 "group.column",
                 "ontology",
                 "dict.path",
                 "column",
                 "denominator.column",
                 "tree.path",
                 "tree.type",
                 "type",
                 "MHT.method",
                 "cores",
                 "spearman.qvalue.cutoff",
                 "pearson.qvalue.cutoff",
                 "kendall.qvalue.cutoff",
                 "linear_model.qvalue.cutoff",
                 "spearman.cor.upper.cutoff",
                 "spearman.cor.lower.cutoff",
                 "pearson.cor.upper.cutoff",
                 "pearson.cor.lower.cutoff",
                 "kendall.cor.upper.cutoff",
                 "kendall.cor.lower.cutoff",
                 "sd.cutoff",
                 "cv.cutoff",
                 "annotation_size.cutoff",
                 "prevalence.cutoff",
                 "heterogeneity.cutoff",
                 "raw_data_sd_filter")]
confs <- data.frame(Parameter = names(confs),
                    Value     = as.character(confs),
                    stringsAsFactors = FALSE)
DT::datatable(confs, 
              options = list(pageLength = 50,
                             searching = FALSE,
                             info = FALSE,
                             ordering = FALSE,
                             dom = "t"))
```
