plotFeatures: Plot splice graph and heatmap of expression values

In ldg21/SGSeq: Splice event prediction and quantification from RNA-seq data

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

ldg21/SGSeq documentation built on Oct. 14, 2020, 9:51 p.m.