splicegrahm2: SpliceGraHM2: two-class splice graph heatmap

In pkimes/spliceclust: Visualization and Clustering of Spliced Components

Description

Splice graphs as disjoint heatmaps for the comparative visualization of splice graphs across multiple samples in a single figure. Differs from splicegrahm by allowing 2 graphs to be drawn in parallel along the horizontal axis flipped along the vertical axis.

Usage

splicegrahm2(obj1, obj2, sort_sep = FALSE, sort_idx1 = 1, sort_idx2 = 1,
  log_base = 10, log_shift = 1, bin = TRUE, genomic = TRUE,
  ex_use = 2/3, flip_neg = TRUE, j_incl = FALSE, use_blk = FALSE,
  eps = 10000, txlist = NULL, txdb = NULL, orgdb = NULL, title = "",
  mirror = TRUE, same_scale = TRUE, ...)

## S4 method for signature 'concomp,concomp'
splicegrahm2(obj1, obj2, sort_sep = FALSE,
  sort_idx1 = 1, sort_idx2 = 1, log_base = 10, log_shift = 1,
  bin = TRUE, genomic = TRUE, ex_use = 2/3, flip_neg = TRUE,
  j_incl = FALSE, use_blk = FALSE, eps = 10000, txlist = NULL,
  txdb = NULL, orgdb = NULL, title = "", mirror = TRUE,
  same_scale = TRUE, ...)

Arguments

obj1	a concomp object
obj2	a concomp object
sort_sep	a logical whether to sort each exon, junction separately (default = FALSE)
sort_idx1	an integer value specifying the order of the obj1 samples in each exon, see details for more information on all possible input, if length is n, then this ordering is used (default = 1)
sort_idx2	an integer value specifying the order of the obj2 samples in each exon, see details for more information on all possible input, if length is n, then this ordering is used (default = 1)
log_base	a numeric specifying the scale of the binning for the plotting 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)
bin	a logical whether to bin the values for easier viewing (default = TRUE)
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)
j_incl	a logical whether to include heatmaps for junctions (default = FALSE)
use_blk	a logical whether to use a black background (default = FALSE)
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)
title	a character string title printed at the top of plot (default = "")
mirror	a logical whether bottom plot should be flipped along vertical axis for 'mirrored' effect (default = TRUE)
same_scale	a logical whether top and bottom plots should be shown on same vertical scaling, i.e. to highlight group size differences (default = TRUE)
...	other parameters to be passed

Details

sort_idx can take values of either:

• 1: sort on first exon

• 2: sort on PC 2

• 3: sort on mean exon coverage

• 4: sort on mean exon log-coverage

• 5: rev sort on mean exon coverage

• 6: rev sort on mean exon log-coverage

Value

a ggplot2 plot showing the splice graph with heatmaps shown at each node and each splice

Author(s)

Patrick Kimes

pkimes/spliceclust documentation built on Jan. 2, 2020, 4:44 a.m.