R/plotGO.R

In fpsanz/enrichGene:

plotGO <- function(enrichdf, nrows = 30, orderby=NULL, ont){
    require(plotly)
    if(!is.data.frame(enrichdf)){
        stop("enrichdf should be data.frame")
    }
    if(!exists("ont") | !(ont %in% c("BP","MF","CC")) ){
        stop("A valid value should be provided for 'ont'")
    }
    dataTitle <- list(BP=c("Biological Process", 'rgb(227,74,51)'),
                      MF=c("Molecular Function",'rgb(31,119,180)'),
                      CC=c("Cellular Component", 'rgb(49,163,84)'))
    enrichdf <- enrichdf[enrichdf$Ont == ont, ]
    if(!is.null(orderby)){
        orderby = match.arg(orderby, c("DE", "P.DE", "N", "Term"))
        if(orderby=="P.DE" | orderby =="Term"){
            enrichdf <- enrichdf %>% arrange(get(orderby))
        } else{ enrichdf <- enrichdf %>% arrange(desc(get(orderby)))}
    }
    p <- enrichdf[1:nrows,] %>%
        plot_ly(x=~DE, y=~go_id, text=~Term, type = "bar",
                marker = list(color=dataTitle[[ont]][2]),
                orientation = "v") %>%
        layout(margin = list(l=100), yaxis = list(title=""),
               title=dataTitle[[ont]][1])
    return(p)
}