plotVariants {SGSeq} | R Documentation

## Plot splice graph and heatmap of splice variant frequencies

### Description

Plot splice graph and heatmap of splice variant frequencies.

### Usage

    plotVariants(x, eventID = NULL, tx_view = FALSE, cex = 1,
      transform = function(x) {     x }, Rowv = NULL, distfun = dist,
      hclustfun = hclust, margin = 0.2, RowSideColors = NULL,
      square = FALSE, cexRow = 1, cexCol = 1, labRow = colnames(x),
      col = colorRampPalette(c("black", "gold"))(256), zlim = c(0, 1),
      heightPanels = c(1, 2), expand_variants = FALSE, ...)

### Arguments

`x` | `SGVariantCounts` object
`eventID` | Single event identifier used to subset `x`
`tx_view` | Plot transcripts instead of splice graph (experimental)
`cex` | Scale parameter for feature labels and annotation
`transform` | Transformation applied to splice variant frequencies
`Rowv` | Determines order of rows. Either a vector of values used to reorder rows, or `NA` to suppress reordering, or `NULL` for hierarchical clustering.
`distfun` | Distance function used for hierarchical clustering of rows (samples)
`hclustfun` | Clustering function used for hierarchical clustering of rows (samples)
`margin` | Width of right-hand margin as fraction of width of the graphics device. Ignored if `square` is `TRUE`.
`RowSideColors` | Character vector (or list of character vectors) with length(s) equal to `ncol(x)` containing color names for horizontal side bars for sample annotation
`square` | Logical, if `TRUE` margins are set such that cells in the heatmap are square
`cexRow` | Scale factor for row (sample) labels
`cexCol` | Scale factor for column (feature) labels
`labRow` | Character vector of row (sample) labels
`col` | Heatmap colors
`zlim` | Range of values for which colors should be plotted, if `NULL` range of finite values
`heightPanels` | Numeric vector of length two indicating height of the top and bottom panels.
`expand_variants` | Experimental option - leave set to `FALSE`
`...` | further arguments passed to `plotSpliceGraph`

### Value

`data.frame` with information on exon bins and splice junctions included in the splice graph

### Author(s)

Leonard Goldstein

### Examples

    ## Not run:
    sgvc_annotated <- annotate(sgvc_pred, txf_ann)
    plotVariants(sgvc_annotated)

    ## End(Not run)
    NULL

[Package SGSeq version 1.28.0 Index]