ctwas_locus_plot: Plot the output of cTWAS at a single locus

In simingz/ctwas: Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits

Plot the output of cTWAS at a single locus

Description

Plot the output of cTWAS at a single locus

Usage

ctwas_locus_plot(
  ctwas_res,
  region_tag,
  outputdir,
  outname,
  focus = NULL,
  xlim = NULL,
  ymax_twas = NULL,
  twas_sig_thresh = NULL,
  alt_names = NULL,
  label_panel = c("both", "cTWAS", "TWAS"),
  label_genes = NULL,
  label_pos = NULL,
  plot_eqtl = NULL,
  legend_panel = c("cTWAS", "TWAS"),
  legend_side = c("right", "left"),
  rerun_ctwas = F,
  rerun_load_only = F,
  return_table = F,
  show_correlations = T,
  z_snp = NULL,
  z_gene = NULL,
  empty_gene_track = F
)

Arguments

ctwas_res	the main output of ctwas_rss as a data frame, with z-scores included
region_tag	a character with format "regiontag1_regiontag2" indicating the reigon to plot; e.g. "16_1"
outputdir	a string, the directory where ctwas output is stored
outname	a string, the output name
focus	the focal gene; points are colored by correlations with this gene. The lead TWAS gene by default
xlim	a vector with the start and end positions to plot, in megabases
ymax_twas	the ymax parameter of the TWAS panel
twas_sig_thresh	the significance threshold for TWAS as a p-value
alt_names	the name of the column that contains alternative gene names in ctwas_res; null by default
label_panel	the panel(s) to plot gene gene names; both cTWAS and TWAS panels by default
label_genes	the gene names to label; all by default
label_pos	a vector of the same length as label_genes indicating the position of the gene labels; 1=below, 2=left, 3=above, 4=right. Above by default.
plot_eqtl	the genes to plot eQTL tracks for; the gene specified by focus by default
legend_panel	the panel to plot the legend in
legend_side	the side to plot the legend on
rerun_ctwas	if TRUE, cTWAS will be re-run at this locus with thin=1 to ensure all variants are plotted
rerun_load_only	if TRUE, the function will look for results generated by rerun_ctwas=T without running cTWAS again
return_table	if TRUE, return the table that underlies the plot
show_correlations	if TRUE, genes and variants are colored by their correlations with focus
z_snp	the z_snp argument supplied to ctwas_rss; required if rerun_ctwas=T
z_gene	the z_gene argument supplied to ctwas_rss; required if rerun_ctwas=T
empty_gene_track	if TRUE, leave space below the plot for the gene track generated by the ctwas_locus_plot_genetrack function

simingz/ctwas documentation built on Sept. 17, 2024, 10:55 p.m.