R/image.lewy.counts.R

In vladpetyuk/LewyBodies.SN.TopDown: What the package does (short line)

#' plots count data
#' 
#' plot count data for Lewy Body project
#' 
#' @param m MSnSet object
#' @param valueName name of the value to be displayed
#' 
#' @import RColorBrewer
#' 
#' @export
#' 
image.lewy.counts <- function(m, valueName='value'){
    
    # scaling counts to [0,1]
    x <- exprs(m)
    x <- sweep(x, 1, apply(x, 1, min), '-')
    x <- sweep(x, 1, apply(x, 1, max), '/')
    exprs(m) <- x
    
    # convertion to long format
    mlong <- melt(exprs(m), varnames=c("Feature", "Sample.ID"),
                  value.name='value')
    mlong$Peptide.ID <- as.character(mlong$Feature)
    mlong$Sample.ID <- as.character(mlong$Sample.ID)
    mlong <- merge(mlong, pData(m), by.x="Sample.ID", by.y="row.names")
    x <- mlong   
    x$Feature <- ordered(x$Feature, levels=rev(sort(unique(x$Feature))))
    
    gLabeller <- function(var, value){
        value <- as.character(value)
        if (var=="subject.type") {
            value[value=="case"] <- "Cases with Lewy Bodies"
            value[value=="control.1"]   <- "Controls, Matched by Neuronal Loss"
            value[value=="control.2"]   <- "Controls, Not Matched by Neuronal Loss"
        }
        return(value)
    }
    
    p <- ggplot(x, aes(x=match.group, y=Peptide.ID, fill=value)) +
        geom_raster() +
        scale_fill_gradientn(
            colours=colorRampPalette(brewer.pal(9,"Blues"))(100)) +
        facet_grid( ~ subject.type, labeller=gLabeller) +
        theme(
            panel.grid.major = element_blank(),
            panel.grid.minor = element_blank(),
            panel.margin = unit(1.5, "lines"),
            panel.border = element_rect(linetype = "dashed",
                                        size=1, colour = "black", fill=NA),
            legend.key.height = unit(2, "lines")
        ) +
        xlab("matching group #") +
        ylab("feature") +
        labs(fill=valueName)
    return(p)
}