peak_overlap_plot: Plot overlap between some SNP group and various epigenomic...

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

Plot overlap between some SNP group and various epigenomic data

Description

Plot overlap between some SNP group and various epigenomic data

Usage

peak_overlap_plot(
  merged_DT,
  snp_filter = "Consensus_SNP==TRUE",
  force_new = FALSE,
  include.NOTT2019_peaks = TRUE,
  include.NOTT2019_enhancers_promoters = TRUE,
  include.NOTT2019_PLACseq = TRUE,
  include.CORCES2020_scATACpeaks = TRUE,
  include.CORCES2020_Cicero_coaccess = TRUE,
  include.CORCES2020_bulkATACpeaks = TRUE,
  include.CORCES2020_HiChIP_FitHiChIP_coaccess = TRUE,
  include.CORCES2020_gene_annotations = TRUE,
  plot_celltype_specificity = TRUE,
  plot_celltype_specificity_genes = FALSE,
  facets_formula = ". ~ Cell_type",
  show_plot = TRUE,
  label_yaxis = TRUE,
  x_strip_angle = 90,
  x_tick_angle = 40,
  drop_empty_cols = FALSE,
  fill_title = paste(snp_filter, "\nin epigenomic peaks"),
  save_path = FALSE,
  height = 11,
  width = 12,
  subplot_widths = c(1, 0.5),
  verbose = TRUE
)

Arguments

force_new	Don't use previously downloaded files.
include.NOTT2019_peaks	Plot SNP subset overlap with peaks from cell-type-specific bulk ATAC, H3K27ac, and H3K4me3 assays.
include.NOTT2019_enhancers_promoters	Plot SNP subset overlap with cell enhancers and promoters.
include.CORCES2020_scATACpeaks	Plot SNP subset overlap with cell-type-specific scATAC-seq peaks.
include.CORCES2020_Cicero_coaccess	Plot SNP subset overlap with Cicero coaccessibility peaks (derived from scATACseq).

Source

Nott et al., 2019 (The Lancet Neurology) Corces et al., 2020 (Nature Genetics)

See Also

Other summarise: CS_bin_plot(), CS_counts_plot(), plot_dataset_overlap(), super_summary_plot()

Examples

#### Data ####
merged_DT <- echodata::get_Nalls2019_merged()

#### Consensus SNPs #####
gg_peaks <- echoannot::peak_overlap_plot(
    merged_DT = merged_DT,
    plot_celltype_specificity = TRUE)
#### UCS SNPs ####
## Not run: 
gg_peaks <- echoannot::peak_overlap_plot(
    merged_DT = merged_DT,
    snp_filter = "Support>0",
    fill_title = "UCS SNPs in epigenomic peaks")

## End(Not run)

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.