add plotSig mixOmicsTeam#134

NAMESPACE

@@ -146,6 +146,7 @@ export(plotArrow)
 export(plotDiablo)
 export(plotIndiv)
 export(plotLoadings)
+export(plotSig)
 export(plotVar)
 export(pls)
 export(plsda)

R/plotSig.R

@@ -0,0 +1,100 @@
+#' Plot the values for signature variables
+#'
+#' Plots the standardaised 'expression' values for the variables for
+#' a given block on a given component.
+#' 
+#' @param object An object of class \code{block.splsda} or \code{block.spls}
+#' @param block Name of the block to use
+#' @param comp Integer, the component to use
+#' @param group Factor, the grouping variable (not required for DA objects)
+#' @param top_n Integer, only show this number of top features
+#' @template arg/col.per.group
+#' @param contrib The contribution type. one of c('max', 'min')
+#' @param global Logical indicating whether to seggregate all features or show
+#'   the global plots.
+#'
+#' @return A ggplot object
+#' @export
+#'
+#' @examples
+#' see ?block.splsda and ?block.spls
+plotSig <-
+    function(object,
+             block,
+             comp = 1,
+             group = NULL,
+             top_n = NULL,
+             col.per.group = NULL,
+             contrib = c('max', 'min'),
+             global = FALSE,
+             title = NULL)
+    {
+
+    contrib <- match.arg(contrib)
+
+    blocks <- names(object$X)
+    if (!block %in% blocks)
+        stop(message = sprintf("block must be one of: %s", paste0(blocks, collapse = ', ')))
+    df <- data.frame(object$X[[block]], check.names = FALSE)
+
+    ## group factor
+    group <- .get.group(group, object, n_ind = nrow(df))
+
+    col.group <- .get.cols.and.group(col.per.group = col.per.group, 
+                                     group = group)
+    group <- col.group$group
+    col.per.group <- col.group$col.per.group
+    vars <- selectVar(object, block=block, comp=comp)[[1]]$value
+    if (contrib == 'max')
+    {
+        vars <- vars[vars$value.var > 0, drop=FALSE, ]
+    } else
+    {
+        vars <- vars[vars$value.var < 0, drop=FALSE, ]
+    }
+    if (is.null(top_n))
+    {
+        top_n <- nrow(vars)
+    } else {
+        top_n <- min(as.integer(top_n), nrow(vars))
+    }
+
+
+    if (top_n < 3)
+    {
+        message("Too few variables match the provided criteria. Aborting the plot.")
+        return(NULL)
+    }
+    vars <- vars[seq_len(top_n),,drop=FALSE]
+    var.names <- rownames(vars)
+    if (!all(var.names %in% colnames(df)))
+        .stop("Unexpected error.\n")
+    df <- df[,var.names]
+    df$group <- group
+    df <-
+        melt(df,
+             id.vars = 'group',
+             variable.name = 'feature',
+             value.name = 'value')
+    df$feature <- factor(df$feature, levels = var.names, ordered = TRUE)
+
+    if (global)
+    {
+        df$feature <- 'plotSig'
+    }
+
+    p <- ggplot(df, aes(group, value, fill=group)) +  
+        geom_violin(adjust=0.9) +
+        geom_boxplot(width=0.1) + 
+        scale_fill_manual(values = col.per.group) + 
+        theme_classic() + 
+        labs(x='', 
+             y='value (standardised)', 
+             title = title) + 
+        theme(legend.position = 'none', 
+              axis.text.x = element_text(angle = 45, vjust = 1, hjust=1), 
+              plot.title = element_text(hjust = 0.5), 
+              strip.background = element_rect(colour="black", fill="grey80")) + 
+        facet_wrap(.~feature)
+    p
+}

examples/block.spls-examples.R

@@ -22,6 +22,14 @@ plotIndiv(TCGA.block.spls, group =  breast.TCGA$data.train$subtype, ind.names =
 # illustrates coefficient weights in each block
 plotLoadings(TCGA.block.spls, ncomp = 1)
 plotVar(TCGA.block.spls, style = 'graphics', legend = TRUE)
+
+## plot signature variables for mrna and mirna
+group <- breast.TCGA$data.train$subtype
+# min contribution for mrna
+plotSig(object = TCGA.block.spls, comp = 1, block = 'mrna', contrib = 'min', group = group)
+# max contribution for protein
+plotSig(object = TCGA.block.spls, comp = 1, block = 'Y', contrib = 'max', group = group)
+
 \dontrun{
 network(TCGA.block.spls)
 }

examples/block.splsda-examples.R

@@ -34,3 +34,11 @@ TCGA.block.splsda$design
 # illustrates coefficient weights in each block
 plotLoadings(TCGA.block.splsda, ncomp = 1, contrib = 'max')
 plotVar(TCGA.block.splsda, style = 'graphics', legend = TRUE)
+
+## plot signature variables for mrna and mirna
+# min contribution for mrna
+plotSig(object = TCGA.block.splsda, comp = 1, block = 'mrna', contrib = 'min')
+## plot only the top 6 variables
+plotSig(object = TCGA.block.splsda, comp = 1, block = 'mrna', contrib = 'min', top_n = 6)
+# max contribution for protein
+plotSig(object = TCGA.block.splsda, comp = 1, block = 'protein', contrib = 'max')