splicegralp: SpliceGraLP: splice graph loadings plot
In pkimes/spliceclust: Visualization and Clustering of Spliced Components

Description Usage Arguments Value Author(s)

Splice graphs with loadings shown along the exons and junctions to illustrate expression patterns across a connected component. The function can be used to illustrate, e.g. differences across groups/clusters or principal component loadings.

splicegralp(obj, e_loads, j_loads = NULL, load_lims = NULL,
  genomic = TRUE, ex_use = 2/3, flip_neg = TRUE, use_blk = FALSE,
  txlist = NULL, txdb = NULL, orgdb = NULL, ...)

## S4 method for signature 'concomp'
splicegralp(obj, e_loads, j_loads = NULL,
  load_lims = NULL, genomic = TRUE, ex_use = 2/3, flip_neg = TRUE,
  use_blk = FALSE, txlist = NULL, txdb = NULL, orgdb = NULL, ...)

`obj`	a `concomp` object with exon and junction information
`e_loads`	a matrix of exon loadings in columns
`j_loads`	a matrix of junction loadings in columns (default = NULL)
`load_lims`	a vector of length 2 that should be used as the bounds on the color scale, e.g. `c(-1, 1)` if plotting PCA loadings
`genomic`	a logical whether genomic coordinates should be used to plot the heatmap (default = TRUE)
`ex_use`	a numeric specifying the proportion of the plot exons should occupy if non-genomic coordinate plotting is desired (default = 2/3)
`flip_neg`	a logical whether to flip plotting of genes on negative strand to run left to right (default = TRUE)
`use_blk`	a logical whether to use a black background (default = FALSE)
`txlist`	a GRangesList of transcripts or genes which should be queried and added to the plot if falling within the region of the connected component (default = NULL)
`txdb`	a transcript database which can be used to query the transcript IDs identified from txlist (default = NULL)
`orgdb`	a database that can be queried using keys obtained from `txdb` to determine corresponding gene symbols (default = NULL)
`...`	other parameters to be passed