plotFeatures {SGSeq} | R Documentation

## Plot splice graph and heatmap of expression values

### Description

Plot splice graph and heatmap of expression values.

### Usage

    plotFeatures(x, geneID = NULL, geneName = NULL, which = NULL,
      tx_view = FALSE, cex = 1, assay = "FPKM", include = c("junctions",
      "exons", "both"), transform = function(x) {     log2(x + 1) },
      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 = NULL, heightPanels = c(1, 2), ...)

### Arguments

`x` | `SGFeatureCounts` object
`geneID` | Single gene identifier used to subset `x`
`geneName` | Single gene name used to subset `x`
`which` | `GRanges` used to subset `x`
`tx_view` | Plot transcripts instead of splice graph (experimental)
`cex` | Scale parameter for feature labels and annotation
`assay` | Name of assay to be plotted in the heatmap
`include` | Include “exons”, “junctions” or “both” in the heatmap
`transform` | Transformation applied to assay data
`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.
`...` | 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:
    sgfc_annotated <- annotate(sgfc_pred, txf_ann)
    plotFeatures(sgfc_annotated)

    ## End(Not run)
    NULL

[Package SGSeq version 1.14.0 Index]