phen_manhattan: phen_manhattan

In SJTU-CGM/vPanG: An R package to analyze and visualize PAV results from pan-genome of "map-to-pan" strategy.

Description

Plot the result of phenotypic association of a certain phenotype in a Manhattan plot.

Usage

phen_manhattan(
  pav_obj,
  phen_stat_res,
  phen_name,
  chr,
  bp,
  adjust_p = T,
  highlight_top_n = 5,
  highlight_text_size = 4,
  point_size = 1.5,
  x_text_size = NULL,
  x_title_size = NULL,
  y_text_size = NULL,
  y_title_size = NULL
)

Arguments

pav_obj	A PAV object.
phen_stat_res	The result from phen_stat.
phen_name	The name of phenotype used for displaying.
chr	The name in 'gene_info' denoting chromosomes.
bp	The name in 'gene_info' denoting chromosomal position.
adjust_p	A logical value indicating whether adjust p_value.
highlight_top_n	The top 'n' points will be highlighted.
highlight_text_size	The size of labels on highlight points.
point_size	The size of points.
x_text_size	The size of tick labels on x-axis.
x_title_size	The size of x-axis title.
y_text_size	The size of tick labels on y-axis.
y_title_size	The size of y-axis title.

SJTU-CGM/vPanG documentation built on Dec. 18, 2021, 11:59 a.m.