splicepcp: SplicePCP: splice graph parallel coordinates plot
In pkimes/spliceclust: Visualization and Clustering of Spliced Components

Description Usage Arguments Value Author(s)

Splice graph expression plot with exons along horizontal axis with vertical axis showing expression level. The plot provides an alternative to the heatmaps used to visualize expression using the splicegrahm and splicegralp functions.

splicepcp(obj, log_base = 10, log_shift = 1, genomic = TRUE,
  ex_use = 2/3, flip_neg = TRUE, imodel = TRUE, highlight = NULL,
  eps = 10000, txlist = NULL, txdb = NULL, orgdb = NULL, ...)

## S4 method for signature 'concomp'
splicepcp(obj, log_base = 10, log_shift = 1,
  genomic = TRUE, ex_use = 2/3, flip_neg = TRUE, imodel = TRUE,
  highlight = NULL, eps = 10000, txlist = NULL, txdb = NULL,
  orgdb = NULL, ...)

`obj`	a `concomp` object
`log_base`	a numeric specifying the scaling of expression values at each exon, which 0 resulting in no long scaling being applied (default = 10)
`log_shift`	a numeric specifying the shift to be used in the log transformation for handling 0 values (default = 1)
`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)
`imodel`	a logical whether to include the connected component plot generated by splicegralp or splicegrahm to the plot (default = TRUE)
`highlight`	a vector of labels to highlight samples in groups or clusters (default = NULL)
`eps`	a numeric value specifying the number of base pairs around `obj` to look for overlapping gene models, if eps = NULL, then all overlapping gene models are included (default = 1e4)
`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