viz_transcripts
Format
cg viz_transcripts ?options? isoform_counts_file gene output_file
Summary
Creates a visual presentation of isoform usage
Description
cg viz_transcripts creates a graphical representation of the
isoforms present in a file for a given gene (using the R package
ggtranscript) together with their counts, percentages, etc.
The result consists of two (linked) panels, the left showing the
isoforms, and the right showing matching numerical fields in a grid
(with cells coloured according to size of number). By default, all
fields in the file starting with count are added to this panel, but
there are options to change/limit this.
By default the isoforms are rescaled, reducing the size of the
much larger introns so they are not obscuring the differences in exon
use (thus intron/exon sizes are not proportional, and numbers on X
axis are not actual location). Optionally this rescaling can be
turned of.
Arguments
- isoform_counts_file
- a file containing isoforms (in the gene tsv format) with numerical info (counts)
about the isoforms
- gene
- selected gene of which isoforms will be visualized
- output_file
- name of output file to be generated (the file extension
deternmines the type of file, .e.g .pdf)
Options
- -countfields 'shortname1 field1 shortname2 field2 ..'
- specify the (numerical) fields to be displayed (field1,
field2, ..) and the names they should be given (shortname1.
shortname2, ..)
- -countfieldpatterns 'pattern1 ..'
- if -countfields is not given, all fields matching one of the
patterns (regular expression) given here will be displayed in the
numerical panel. Standard the field name will be used to name a
column in the grid, but if the pattern has parts between
parenthesis, these will be extracted to make the name, example of
such a pattern:
counts_weighed-(Excitatory_neurons).*_splice-(.*)_v6.5
- -rescale 0/1
- rescale to reduce effect large introns (1) or give a
proportional visualization (0)
- -sortcol colname
- sort on the given column, default is to sort on the first,
set to '' to not sort
- -proportions 0/1
- convert the values to proportions (in percent)
- -textsize
- text size of the numbers in the grid (default 10, set to 0 to
remove numbers)
- -panelwidths 'w1 w2'
- list of panel widths (default '3 1'). determines the relative
size of left and right panel
- -width
- width in mm of the results
- -height
- height in mm of the results
Category
Visualization