get_ase_data_matrix_heatmap: Generate a heatmap for a given list of ASE.

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Generate a heatmap for a given list of ASE.

Description

Generate a heatmap for a given list of ASE.

Usage

get_ase_data_matrix_heatmap(
  se,
  event_names,
  samples,
  column_condition = "condition",
  method = "PSI",
  summarise_groups = TRUE,
  summarise_groups_by = "mean",
  show_row_names = FALSE,
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  show_column_dend = FALSE,
  show_row_dend = FALSE,
  ...
)

Arguments

se	an object of class NxtSE.
event_names	a character vector denoting valid spliceWiz event names.
samples	a character vector denoting valid sample names.
column_condition	a name of column in se storing condition. Deafault: "condition".
method	one of the character strings: "Z-score", "PSI" ,"logit".
summarise_groups	pass to summarise_groups of get_ASE_data_matrix().
summarise_groups_by	pass to summarise_groups_by of get_ASE_data_matrix().
show_row_names	logical, whether to show row names in the heatmap.
cluster_rows	logical, whether to clusters rows in the heatmap.
cluster_columns	logical, whether to cluster column in the heatmap or not.
show_column_dend	logical, whether to show column dendrogram in the heatmap or not.
show_row_dend	logical, whether to show row dendrogram in the heatmap or not.
...	other parameters to pass ComplexHeatmap::Heatmap()

Value

a heatmap

Examples

se <- SpliceWiz::SpliceWiz_example_NxtSE(novelSplicing = TRUE)
SpliceWiz::colData(se)$treatment <- rep(c("A", "B"), each = 3)
SpliceWiz::colData(se)$replicate <- rep(c("P","Q","R"), 2)
res <- run_ase_diff_analysis(x = se, test_factor = "treatment", test_nom = "A" ,test_denom = "B",  IRmode ="annotated",  cutoff_lfc = 0.6, cutoff_padj = 1, regul_based_upon = 2)
event_names = get_ASEsets_by_regulation(x = res, sample_comparisons = "A_VS_B", regul = "all") %>% unlist()

get_ase_data_matrix_heatmap(se, event_names = event_names, samples = c("A" ,"B"), column_condition = "treatment", summarise_groups = FALSE )
get_ase_data_matrix_heatmap(se, event_names = event_names, samples = c("A" ,"B"), column_condition    = "treatment", summarise_groups = TRUE )
get_ase_data_matrix_heatmap(se, event_names = event_names, samples = c("P" ,"R","Q"), column_condition    = "replicate",method = "Z-score", cluster_rows = TRUE)
get_ASE_data_matrix(se, event_names , samples = c("A", "B"), column_condition ="treatment")

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.