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

In whweve/wisassoplot2: visualize genome-wide association study with gene annotation and linkage disequiblism

Description

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

Usage

plot_gene(transcript, gtf, association, hapmap, hapmap_ld = NULL,
  slide_length = -1, threadN = 1, up = NULL, down = NULL,
  threshold = NULL, ldstatistics = "rsq", leadsnp = NULL,
  link2gene = TRUE, triangleLD = TRUE, link2LD = TRUE,
  leadsnpLD = TRUE, exon_colour = "gray", cds_colour = "black",
  utr_colour = "gray", intron_colour = "gray", colour02 = "gray",
  colour04 = "cyan", colour06 = "green", colour08 = "yellow",
  colour10 = "red")

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	link the locis that passed the threshold to the genic structure, default TRUE.
triangleLD	show LD in the format lile triangle, default TRUE.
link2LD	link the locis that passed the threshold to the LD, default TRUE.
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.

Value

ggplot2 plot

Author(s)

Hongwei Wang <[e-mail]>

Examples

data(gtf)
data(zmvpp1_association)
data(zmvpp1_hapmap)
plot_gene('GRMZM2G170927_T01',gtf,association=zmvpp1_association,hapmap=zmvpp1_hapmap,hapmap_ld = zmvpp1_hapmap,threshold=8,up=500,down=600,leadsnpLD = FALSE)

whweve/wisassoplot2 documentation built on May 15, 2019, 9:56 p.m.