R/genePlots.R

In lpantano/DEGreport: Report of DEG analysis

#' Make nice colors for metadata
#' 
#' The function will take a metadata table and use Set2 palette when
#' number of levels is > 3 or a set or orange/blue colors other wise.
#' 
#' @param ann Data.frame with metadata information. Each column will be used to 
#'   generate a palette suitable for the values in there.
#' @param col_fun Whether to return a function for continuous variables 
#'   (compatible with [ComplexHeatmap::HeatmapAnnotation()]) or
#'   the colors themself (comparible with [pheatmap::pheatmap())]).
#' @param con_values Color to be used for continuous variables.
#' @param cat_values Color to be used for 2-levels categorical variables.
#' @param palette Palette to use from `brewer.pal()` for
#'   multi-levels categorical variables.
#' @examples 
#' data(humanGender)
#' library(DESeq2)
#' library(ComplexHeatmap)
#' idx <- c(1:10, 75:85)
#' dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:10, idx],
#'   colData(humanGender)[idx,], design=~group)
#' th <- HeatmapAnnotation(df = colData(dse),
#'                        col = degColors(colData(dse), TRUE))
#' Heatmap(log2(counts(dse)+0.5), top_annotation = th)
#' 
#' custom <- degColors(colData(dse), TRUE,
#'           con_values = c("white", "red"),
#'           cat_values = c("white", "black"),
#'           palette = "Set1")
#' th <- HeatmapAnnotation(df = colData(dse),
#'                         col = custom)
#' Heatmap(log2(counts(dse)+0.5), top_annotation = th)
#' @export
degColors <- function(ann, col_fun = FALSE,
                      con_values = c("grey80", "black"),
                      cat_values = c("orange", "steelblue"),
                      palette = "Set2"){
    col <- lapply(names(ann), function(a){
        if (class(ann[[a]][1])[1] == "numeric"){
            fn = colorRamp2(c(min(ann[[a]]),
                              max(ann[[a]])),
                            con_values)
            if (col_fun){
                return(fn)
            }else{
                return(fn(ann[[a]]))
            }
        }
        
        if (length(unique(ann[[a]])) < 3){
            v <- cat_values[1:length(unique(ann[[a]]))]
            names(v) <- unique(ann[[a]])
            return(v)
        }
        v <- brewer.pal(length(unique(ann[[a]])), palette)
        names(v) <- unique(ann[[a]])
        v
    })
    names(col) <- names(ann)
    col
}


#' Plot top genes allowing more variables to color and shape points
#'
#' @param dds [DESeq2::DESeqDataSet] object or SummarizedExperiment
#'   or Matrix or data.frame. In case of a DESeqDataSet object, always
#'   the normalized expression will be used
#'   from `counts(dds, normalized = TRUE)`.
#' @param res [DESeq2::DESeqResults] object.
#' @param n Integer number of genes to plot from the `res` object. It will
#'   take the top N using padj values to order the table.
#' @param genes Character of gene names matching rownames of count data.
#' @param xs Character, colname in colData that will be used as X-axes.
#' @param group Character, colname in colData to color points and add different
#'   lines for each level.
#' @param batch Character, colname in colData to shape points, normally used by
#'   batch effect visualization.
#' @param ann Columns in rowData (if available) used to print gene names. First
#'   element in the vector is the column name in rowData that matches the
#'   row.names of the `dds` or `count` object. Second element in the vector
#'   is the column name in rowData that it will be used as the title for each
#'   gene or feature figure.
#' @param metadata Metadata in case dds is a matrix.
#' @param slot Name of the slot to use to get count data.
#' @param log2 Whether to apply or not log2 transformation.
#' @param xsLab Character, alternative label for x-axis (default: same as xs)
#' @param ysLab Character, alternative label for y-axis..
#' @param color Color to use to plot groups. It can be one color, or a palette
#'   compatible with `ggplot2::scale_color_brewer()`.
#' @param groupLab Character, alternative label for group (default: same as group).
#' @param batchLab Character, alternative label for batch (default: same as batch).
#' @param sizePoint Integer, indicates the size of the plotted points (default 1).
#' @return ggplot showing the expresison of the genes
#' @examples 
#' data(humanGender)
#' library(DESeq2)
#' idx <- c(1:10, 75:85)
#' dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
#'   colData(humanGender)[idx,], design=~group)
#' dse <- DESeq(dse)
#' degPlot(dse, genes = rownames(dse)[1:10], xs = "group")
#' degPlot(dse, genes = rownames(dse)[1:10], xs = "group", color = "orange")
#' degPlot(dse, genes = rownames(dse)[1:10], xs = "group", group = "group",
#'         color = "Accent")
#' @export
degPlot = function(dds, xs, res = NULL, n = 9, genes = NULL,
                   group = NULL, batch = NULL,
                   metadata = NULL,
                   ann = c("geneID", "symbol"),
                   slot = 1L,
                   log2 = TRUE,
                   xsLab = xs,
                   ysLab = "abundance",
                   color = "black",
                   groupLab = group, batchLab = batch,
                   sizePoint = 1){
    if (class(dds)[1] %in% c("data.frame", "matrix"))
        dds = SummarizedExperiment(assays = SimpleList(counts = as.matrix(dds)),
                                   colData = metadata)
    
    if ( !("assays" %in% slotNames(dds)) )
        stop("dds object doesn't have assays slot")
    
    if (!is.null(res))
        res <- res[order(res$padj),] %>% .[!is.na(res$padj),]
    
    if (is.null(genes))
        genes =  row.names(res)[1L:n]
    
    anno <- as.data.frame(rowData(dds))
    
    metadata = data.frame(colData(dds))
    if (class(dds)[1] == "DESeqDataSet")
        counts <- counts(dds, normalized = TRUE)
    else counts <- assays(dds)[[slot]]
    
    stopifnot(class(counts)[1] == "data.frame" | class(counts)[1] == "matrix")
    
    if (log2 & max(counts) < 500L)
        warning("Data seems to be already in log2. Please use log2 = FALSE.")
    if (log2){
        counts <- log2(counts + 0.2)
        ysLab <- paste("log2", ysLab)
    }

    newgenes <- genes
    if (ncol(anno) > 0) {
        name <- intersect(names(anno), ann)
        if (length(name) != 2L)
            message("No genes were mapped to rowData. check ann parameter values.")
        if (length(name) == 2L)
            newgenes <- anno[match(genes, anno[, ann[1L]]), ann[2L]]
        if (sum(is.na(newgenes)) > 0)
            warning(sum(is.na(newgenes)), " cannot be mapped to ", name[2L], 
                    ". Those will be skipped.")
    }
    
    dd <- melt(as.data.frame(counts[genes, , drop = FALSE]) %>%
                  mutate(gene = factor(newgenes, levels=newgenes)))
    colnames(dd) = c("gene", "sample", "count")
    
    dd <-dd[!is.na(dd[["gene"]]),]
    
    dd$xs = as.factor(metadata[as.character(dd$sample), xs])
    
    if (!is.null(group)) {
        dd[, groupLab] = as.factor(metadata[as.character(dd$sample), group])
    }else {
        groupLab = "fake"
        dd[, groupLab] = "fake"
    }
    
    if (!is.null(batch)) {
        dd[, batchLab] = as.factor(metadata[as.character(dd$sample), batch])
        
        p = ggplot(dd, aes_string(x = "xs", y = "count", color = groupLab,
                                  shape = batchLab))
    }else{
        p = ggplot(dd, aes_string(x = "xs", y = "count", color = groupLab))
    }
    
    p = p +
        # geom_violin(alpha=0.3) +
        stat_smooth(fill = "grey80", method = 'loess') +
        geom_point(size = sizePoint, alpha = 0.7,
                   position = position_jitterdodge(dodge.width = 0.9)) +
        facet_wrap(~gene, scales = "free_y") +
        xlab(xsLab) +
        ylab(ysLab)
    if (length(unique(dd[, groupLab])) == 1L) {
        stopifnot(length(color) == 1)
        p = p +
            scale_color_manual(guide = "none", values = color) +
            scale_fill_manual(guide = "none", values = color)
    }else{
        if (color == "black")
            color = "Set1"
        p = p +
            scale_color_brewer(palette = color) +
            scale_fill_brewer(palette = color)
    }
    p = p + theme_bw() +
        theme(strip.background = element_rect(fill = "white"),
              strip.text = element_text(colour = "black"))
    
    suppressWarnings(p)
}

#' Plot selected genes on a wide format
#'
#' @param counts [DESeq2::DESeqDataSet] object or expression matrix
#' @param genes character genes to plot.
#' @param group character, colname in colData to color points and add different
#' lines for each level
#' @param metadata data.frame, information for each sample. Not needed if
#' [DESeq2::DESeqDataSet] given as counts.
#' @param batch character, colname in colData to shape points, normally used by
#' batch effect visualization
#' @return ggplot showing the expresison of the genes on the x
#' axis
#' @examples
#' data(humanGender)
#' library(DESeq2)
#' idx <- c(1:10, 75:85)
#' dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
#'   colData(humanGender)[idx,], design=~group)
#' dse <- DESeq(dse)
#' degPlotWide(dse, rownames(dse)[1:10], group = "group")
#' @export
degPlotWide <- function(counts, genes, group, metadata=NULL, batch=NULL){
    if (is.null(metadata))
        metadata = data.frame(colData(counts))
    metadata = data.frame(metadata)
    if (class(counts)[1] == "DESeqDataSet") {
        dd = bind_rows(lapply(genes,function(gene){
            plotCounts(counts, gene,
                       intgroup = group, returnData = TRUE) %>%
                mutate(count = log2(count + 1)) %>%
                mutate(gene = gene, sample = row.names(metadata))}))
        dd$group = dd[[group]]
    }else if (class(counts)[1] == "matrix") {
        dd = melt(counts[genes, ])
        colnames(dd) = c("gene", "sample", "count")
        dd$group = as.factor(metadata[as.character(dd$sample), group])
    }else{
        stop("No supported for class", class(counts)[1])
    }
    if (is.null(group)) {
        dd$treatment = "one_group"
    }else{
        dd$treatment = dd[,"group"]
    }
    p = ggplot(dd, aes_string(x = "gene", y = "count", color = "treatment"))
    if (!is.null(batch)) {
        dd$batch = as.factor(metadata[dd$sample, batch])
        p = ggplot(dd, aes_string(x = "gene", y = "count",
                                  color = "treatment", shape = "batch"))
    }
    
    p = p +
        geom_point(position = position_jitterdodge(dodge.width = 0.9)) +
        xlab("Genes") +
        ylab("Normalized Counts") +
        theme_bw() +
        theme(axis.text.x = element_text(angle = 45L, hjust = 1L))
    p
}