SGSeq (version 1.6.2)

plotFeatures: 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 parameters passed to plotSpliceGraph

Value

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

Examples

sgfc_annotated <- annotate(sgfc_pred, txf_ann)
plotFeatures(sgfc_annotated)
NULL