plotFeatures {SGSeq} | R Documentation |
Plot splice graph and heatmap of expression values.
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), ...)
x |
|
geneID |
Single gene identifier used to subset |
geneName |
Single gene name used to subset |
which |
|
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 |
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 |
RowSideColors |
Character vector (or list of character vectors)
with length(s) equal to |
square |
Logical, if |
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 |
heightPanels |
Numeric vector of length two indicating height of the top and bottom panels. |
... |
further arguments passed to |
data.frame
with information on exon bins and
splice junctions included in the splice graph
Leonard Goldstein
## Not run: sgfc_annotated <- annotate(sgfc_pred, txf_ann) plotFeatures(sgfc_annotated) ## End(Not run) NULL