heatmap_clones_gene_pat {GeneAccord} | R Documentation |
This function plots the heatmaps of final gene clone matrices.
heatmap_clones_gene_pat(pairs_of_interest, clone_tbl, all_genes_tbl, first_clone_is_N = FALSE, output_pdf = "direct")
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 |
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
|
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" |
After running the GeneAccord
, one may want to visualize
the gene clone
heatmap for significant gene pairs.
None, the function plots a gene-to-clone assignment heatmap.
Ariane L. Moore
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)