heatmap_clones_gene_pat: Heatmaps of gene pairs of interest

In GeneAccord: Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Description

This function plots the heatmaps of final gene clone matrices.

Usage

heatmap_clones_gene_pat(pairs_of_interest, clone_tbl, all_genes_tbl,
  first_clone_is_N = FALSE, output_pdf = "direct")

Arguments

pairs_of_interest	The tibble containing the pairs of genes/pathways that should be visualized in the heatmap. This may be, e.g. the gene pairs were mle_delta > 0, qval < 0.1, and num_patients > 1. It contains the columns 'entity_A', and 'entity_B', and can be generated with GeneAccord. For the plot, the function will attempt to map the gene ID's from ensembl ID to gene name. However, if the input genes are not ensembl IDs, it does not matter.
clone_tbl	The tibble containing the information of which gene/pathway is mutated in which clone from which patient. Here, it is assumed that only one tree from the collection of trees was chosen per patient.
all_genes_tbl	A tibble with all genes ensembl id's and hgnc symbols. Can be created with create_ensembl_gene_tbl_hg.
first_clone_is_N	Logical indicating whether the first clone column is actually representing the normal or germline, and is not a tumor clone. In that case, it will have the name 'N', and all other columns will be one clone number smaller, e.g. 'clone2' is then actually 'clone1' etc. Default: FALSE.
output_pdf	The name of the pdf to be generated. Or if output_pdf is "direct", then the plot is generated directly and not to a pdf. Default: "direct"

Details

After running the GeneAccord, one may want to visualize the gene clone heatmap for significant gene pairs.

Value

None, the function plots a gene-to-clone assignment heatmap.

Author(s)

Ariane L. Moore

Examples

pairs_of_interest <- dplyr::tibble(entity_A="SETD2",
                           entity_B="BAP1")
clone_tbl <- dplyr::tibble(
               file_name=c("X.csv", "X.csv", "Y.csv", "Y.csv"),
               patient_id=c("X", "X", "Y", "Y"),
               altered_entity=c("SETD2", "BAP1", "SETD2", "BAP1"),
               clone1=c(0, 1, 1, 0),
               clone2=c(1, 0, 0, 1))
## Not run: all_genes_tbl <- create_ensembl_gene_tbl_hg()
all_genes_tbl_example <- dplyr::tibble(
                 ensembl_gene_id=c("ENSG00000181555", 
                 "ENSG00000163930"),
                 hgnc_symbol=c("SETD2", "BAP1"))
heatmap_clones_gene_pat(pairs_of_interest, clone_tbl, 
all_genes_tbl_example)

Example output

GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.