trancriptVis: trancriptVis

Description

This package is to visualize gene diffrent isoforms.

Value

A ggplot object.

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').

Author

Junjun Lao

Examples

Run this code

##############################################################
# 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')

Run the code above in your browser using DataLab