---
title: "4.3 - Motif enrichment plots"
output: 
  html_document:
    self_contained: true
    number_sections: no
    theme: flatly
    highlight: tango
    mathjax: null
    toc: FALSE
    toc_float: FALSE
    toc_depth: 2
    css: style.css
  
bibliography: bibliography.bib    
vignette: >
  %\VignetteIndexEntry{"4.3 - Motif enrichment plots"}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---


```{r, echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE}
library(ELMER)
library(DT)
library(dplyr)
library(BiocStyle)
```
<br>

# Motif enrichment plot
Motif  enrichment plot shows the enrichment levels for the selected motifs. 

The plot shows the Odds Ratio (x axis) for the selected motifs with OR above 1.3 and lower boundary of OR above 1.1. The range shows the 95% confidence interval for each Odds Ratio
```{r results='hide', eval=TRUE, fig.height=6,fig.cap="The plot shows the Odds Ratio (x axis) for the selected motifs with OR above 1.3 and lower boundary of OR above 1.3. The range shows the 95% confidence interval for each Odds Ratio."}
motif.enrichment.plot(motif.enrichment = "result/getMotif.hypo.motif.enrichment.csv", 
                      significant = list(OR = 1.5,lowerOR = 1.3), 
                      label = "hypo", 
                      save = FALSE)  
```

```{r results='hide', eval=TRUE, fig.height=10,fig.cap="The plot shows the Odds Ratio (x axis) for the selected motifs with OR above 1.3 and lower boundary of OR above 1.3. The range shows the 95% confidence interval for each Odds Ratio."}
motif.enrichment.plot(motif.enrichment = "result/getMotif.hypo.motif.enrichment.csv", 
                      significant = list(OR = 1.5,lowerOR = 1.3), 
                      label = "hypo", 
                      summary = TRUE,
                      save = FALSE)  
```
