Plot all the Peak2Gene links with heatmap.

Plot all the Peak2Gene links with heatmap.

plotP2GHeatmap(
  p2g_res,
  cor_cutoff,
  atac_matrix,
  rna_matrix,
  cluster_N = 4,
  raster = F,
  palATAC = NA,
  palRNA = NA,
  save_path = NA,
  fig_width = 12,
  fig_height = 12
)

Arguments

p2g_res

The peak2gene result obtained by **getPeak2Gene**

cor_cutoff

Pearson's correlation coefficient threshold for determining significance Peak2Gene links.

atac_matrix

The normalized ATAC-seq data frame obtained by **quantification**. Same as **getPeak2Gene** parameter.

rna_matrix

The normalized RNA-seq data frame. Same as **getPeak2Gene** parameter.

cluster_N

Clustering rows into N modules. Default: 4.

raster

Wheather to raster the plot. Default: FALSE.

palATAC

The color of ATAC heatmap.

palRNA

The color of RNA heatmap.

save_path

The path to save result.

fig_width

The PDF width. Default: 12.

fig_height

The PDF height. Default: 12.

Examples

  plotP2GHeatmap("./P2G_all_links.rds",cor_cutoff=0.4,atac_matrix="./ATAC_norm_quant.tsv",rna_matrix="./RNA_norm_quant.tsv",save_path="./")
#> Error in checkGeAnno(): Necessary Annotation not exist. Please **addAnnotation** first.