IntGenicPlot: plot association with LD and annotation at a given gene

In whweve/IntAssoPlot: visualize genome-wide association study with gene annotation and linkage disequiblism

plot association with LD and annotation at a given gene

Description

This function plot the association with linkage disequiblism and annotation at the level of a single gene.

Usage

IntGenicPlot(
  transcript,
  gtf,
  association,
  hapmap,
  hapmap_ld = NULL,
  slide_length = -1,
  threadN = 1,
  up = NULL,
  down = NULL,
  threshold = NULL,
  ldstatistics = "rsquare",
  leadsnp = NULL,
  link2gene = NULL,
  triangleLD = TRUE,
  link2LD = NULL,
  leadsnpLD = TRUE,
  exon_colour = "gray",
  cds_colour = "black",
  utr_colour = "gray",
  intron_colour = "gray",
  colour02 = "gray",
  colour04 = "cyan",
  colour06 = "green",
  colour08 = "yellow",
  colour10 = "red",
  leadsnp_shape = 23,
  leadsnp_colour = "black",
  leadsnp_fill = "purple",
  leadsnp_size = 1.5,
  marker2highlight = NULL,
  marker2label = NULL,
  marker2label_angle = 60,
  marker2label_size = 1
)

Arguments

transcript	the transcript of gene, required.
gtf	the annotation file, required.
association	the association table, required.
hapmap	the genotype file for computing leadsnpLD in the format of hapmap. The file should be the same file used for coumputing association. required.
hapmap_ld	the genotype file for computing trangleLD in the format of hapmap, not required. If hapmap_ld was not provided, hapmap would be used.
slide_length	the sliding window length for computing LD, default -1.
threadN	the number of (CPU) cores used for computing LD, default 1.
up	the upper distance from the start position of gene
down	the down distance from the end position of gene
threshold	the significant level of the assocition, default NULL.
ldstatistics	the statistics used for computing LD, default rsquare, and the optional is dprime.
leadsnp	snp name provided by user
link2gene	a dataframe speicify markers to be linked from GWAS to genic structure, default NULL. When link2gene is 'NULL', locis that passed the threshold will be linked. Please see help('marker2link').
triangleLD	show LD in the format lile triangle, default TRUE.
link2LD	a dataframe speicify markers to be linked from genic structure to LD matrix, default NULL. When link2gene is 'NULL', locis that passed the threshold will be linked. Please see help('marker2link').
leadsnpLD	show LD of the locis when compared with the most significant loci, default TRUE.
exon_colour	the colour of exon, default gray.
cds_colour	the colour of cds, default black.
utr_colour	the colour of utr, default gray.
intron_colour	the colour of intron, default gray.
colour02	the colour of LD statistics ranged between 0.0 and 0.2, default gray.
colour04	the colour of LD statistics ranged between 0.2 and 0.4, default cyan.
colour06	the colour of LD statistics ranged between 0.4 and 0.6, default green.
colour08	the colour of LD statistics ranged between 0.6 and 0.8, default yellow.
colour10	the colour of LD statistics ranged between 0.8 and 1.0, default red.
leadsnp_shape	the shape of leadsnp, default 23. For others, please see help('points').
leadsnp_colour	the shape of the point of leadsnp, default black. For others, please see help('points').
leadsnp_fill	the filled colour of the point of leadsnp, default purple. For others, please see help('points').
leadsnp_size	the size of of the point of leadsnp, default 1.5. For others, please see help('points').
marker2highlight	a dataframe speicify markers to be showed by colour,shape,fill,size, default NULL. Please see help('marker2highlight').
marker2label	a dataframe speicify markers to be labeled, default NULL. Please see help('marker2link')
marker2label_angle	angel of labeled text, default 60.
marker2label_size	size of labeled text, default 1.

Value

ggplot2 plot

Author(s)

Hongwei Wang <[e-mail]>

Examples

data(gtf)
data(zmvpp1_association)
data(zmvpp1_hapmap)
data(marker2highlight)
data(marker2link)
IntGenicPlot('GRMZM2G170927_T01',gtf,association=zmvpp1_association,hapmap=zmvpp1_hapmap,
hapmap_ld = zmvpp1_hapmap,threshold=8,up=500,down=600,leadsnpLD = FALSE,
marker2highlight=marker2highlight,link2gene=marker2link,link2LD=marker2link,
marker2label=marker2link,marker2label_angle=60,marker2label_size=2)

whweve/IntAssoPlot documentation built on Feb. 19, 2024, 10:14 a.m.