SGSeq (version 1.0.6)

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, toscale = c("exon", "none", "gene"), color = "grey", color_novel = "red", color_alpha = 0.8, color_labels = FALSE, border = "fill", cexLab = 1, cexExon = 1, score = NULL, score_color = "darkblue", score_ylim = NULL, score_ypos = c(0.2, 0.1), score_nbin = 400, main = NULL, cexMain = 1, tx_view = FALSE, tx_dist = 0.1, tx_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, heightTopPanel = 0.3)

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

toscale

Controls which parts of the splice graph are drawn to scale. Possible values are “none” (exonic and intronic regions have constant length), “exon” (exonic regions are drawn to scale) and “gene” (both exonic and intronic regions are drawn to scale).

color

Color used for plotting the splice graph. Ignored if features elementMetadata column “color” is not NULL.

color_novel

Features with missing annotation are highlighted in color_novel. Ignored if features elementMetadata column “color” is not NULL.

color_alpha

Controls color transparency

color_labels

Logical indicating whether label colors should be the same as feature colors

border

Determines the color of exon borders, can be “fill” (same as exon color), “none” (no border) or a valid color name

cexLab

Scale factor for feature labels

cexExon

Scale factor for exon height

score

RLeList containing nucleotide-level scores to be plotted with the splice graph

score_color

Color used for plotting scores

score_ylim

y-axis range used for plotting scores

score_ypos

Numeric vector of length two, indicating the vertical position and height of the score panel, specificed as fractions of the height of the plotting region

score_nbin

Number of bins for plotting scores

main

Plot title

cexMain

Scale factor for plot title

tx_view

Plot transcripts instead of splice graph (experimental)

tx_dist

Vertical distance between transcripts as fraction of height of plotting region

tx_cex

Scale factor for transcript labels

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

heightTopPanel

Height of top panel as fraction of height of the graphics device

Value

Return value of plotSpliceGraph

Examples

## Not run: 
#   sgfc_annotated <- annotate(sgfc, txf)
#   plotFeatures(sgfc_annotated)
# ## End(Not run)