trancriptVis {transPlotR}

trancriptVis

Description

This package is to visualize gene diffrent isoforms.

Arguments

gtfFile

GTF file.

gene

Target gene to plot.

myTranscript

Specify which transcripts to plot use transcipt id.

Chr

Chromosome number.

posStart

Region start position on genome.

posEnd

Region end position on genome.

collapse

Whether to collapse multiple transcripts into one, default(FALSE).

exonWidth

Exon width to plot, default(0.3).

relTextDist

Transcripts name or gene name relative to exon, default(0.3).

intronSize

Intron line size, default(0.5).

arrowBreak

How many gap distance to draw arrows, the smaller the more arrows, default(0.15).

exonColorBy

Whether color group by "transcript_id" or "gene_name", default(NULL).

exonFill

Exon fill color, default('#333399').

circle

Whether make plot into a circle plot, default(FALSE).

cicStart

Circle plot start position, default(pi).

circSegCol

Circle sgement color, default('#333399').

text_only

When circle plot labeled by gene name, whether remove the line connected with gene name, default(FALSE).

ylimLow

The Y axis lower limitation of Circle plot, default(-10).

openAngle

The gap of the circle plot, default(0.5).

arrowCol

Normal arrow color, default('#333399').

arrowAngle

Normal arrow angle, default(30).

arrowLength

Normal arrow length, default(0.1).

arrowType

Normal arrow type, default('open').

addNormalArrow

Whether add normal arrow on plot, default(TRUE).

newStyleArrow

Whether add new style arrow on plot, default(FALSE).

absSpecArrowLen

Whether make new style arrow length to be relative to each transcript length or absolute length to the longest transcript, default(FALSE).

speArrowRelPos

The relative position to the transcript on horizontal direction of new style arrow, default(0).

speArrowRelLen

The relative length to the transcript length of new style arrow, default(0.05).

speArrowStart

The new style arrow start position on the vertical direction, default(-0.15).

speArrowRelHigh

The relative height of new style arrow to the vertical length, default(2).

speArrowLineSize

The new style arrow line size, default(0.5).

speArrowCol

The new style arrow line color, default('black').

speArrowAngle

The new style arrow angle, default(30).

speArrowLen

The new style arrow length, default(0.1).

speArrowType

The new style arrow type, default('closed').

textLabel

The text label aesthetic mappings, default('transcript_id').

textLabelSize

The text label size, default(5).

textLabelColor

The text label color, default('black').

base_size

Theme basesize, default(14).

marginX

Plot left and right margins, default(0.2).

marginY

Plot top and bottomn margins, default(0.2).

aspect.ratio

Plot ratio, default(NULL).

facetByGene

Whether facet by gene to plot, this useful for your genes which are far away from each other or not located on the same chromosome, default(FALSE).

ncolGene

The column numbers to plot, default(NULL).

scales

Facet plot scales, same as "facet_wrap" function, default('free').

strip.position

Facet plot strip.position, same as "facet_wrap" function, default('top').

forcePosRel

Whether force the genome coordinate to relative position to transcript start/end position, default('FALSE').

panel.spacing

Facet plot panel space, default(0.3).

revNegStrand

Whether reverse the negtive strand when set "forcePosRel=TRUE", default('FALSE').

Value

A ggplot object.

Author(s)

Junjun Lao

Examples

##############################################################
# test function

########################################################
# load data
data(gtf)

# non-coding gene
trancriptVis(gtfFile = gtf,
             gene = 'Xist')

# coding gene
trancriptVis(gtfFile = gtf,
             gene = 'Nanog')

# change fill color
trancriptVis(gtfFile = gtf,
             gene = 'Nanog',
             exonFill = '#CCFF00')

# change inrton line size
trancriptVis(gtfFile = gtf,
             gene = 'Nanog',
             intronSize = 1)

# change label size,color and position
trancriptVis(gtfFile = gtf,
             gene = 'Nanog',
             textLabelSize = 4,
             textLabelColor = 'red',
             relTextDist = 0)

# aes by gene name
trancriptVis(gtfFile = gtf,
             gene = 'Nanog',
             textLabel = 'gene_name')

# color aes by transcript
trancriptVis(gtfFile = gtf,
             gene = 'Tpx2',
             exonColorBy = 'transcript_id')

# change arrow color and type
trancriptVis(gtfFile = gtf,
             gene = 'Nanog',
             arrowCol = 'orange',
             arrowType = 'closed')

# no intron gene and add arrow color
# change arrow color and type
trancriptVis(gtfFile = gtf,
             gene = 'Jun',
             textLabel = 'gene_name',
             arrowCol = 'white',
             arrowType = 'closed') +
  theme_void()

# add arrow breaks
trancriptVis(gtfFile = gtf,
             gene = 'Nanog',
             arrowCol = 'orange',
             arrowType = 'closed',
             arrowBreak = 0.1)

# draw specific transcript
p1 <- trancriptVis(gtfFile = gtf,
                   gene = 'Commd7')

p2 <- trancriptVis(gtfFile = gtf,
                   gene = 'Commd7',
                   myTranscript = c('ENSMUST00000071852','ENSMUST00000109782'))

# combine
cowplot::plot_grid(p1,p2,ncol = 2,align = 'hv')