draw_profiles: Draw expression profiles of a clustering

In OceaneCsn/DIANE: DIANE

Draw expression profiles of a clustering

Description

Draw expression profiles of a clustering

Usage

draw_profiles(
  data,
  membership,
  conds = unique(stringr::str_split_fixed(colnames(data), "_", 2)[, 1]),
  expression = "profiles",
  k = NULL,
  nrow = 3
)

Arguments

data	normalized counts with genes as rownames and samples as columns
membership	membership item of the coseq object returned by run_coseq() object
conds	conditions on which to display clustering profiles. Must be a unique vector containing the conditions you want to consider for gene clustering, without the replicate information (string before the underscore in sample names). Default is all the conditions.
expression	if it is set to "profiles" (default), plots expression/sum(expression). if "counts", plots log(Counts+1)
k	if NULL (default), plots all the clusters. Else, plot the clusters in the vetcor k.
nrow	on how many rows display the cluster profiles if k is NULL

Examples

data("abiotic_stresses")
DIANE::draw_profiles(data = abiotic_stresses$normalized_counts, 
membership = abiotic_stresses$heat_DEGs_coseq_membership,
conds = unique(abiotic_stresses$conditions)) 
DIANE::draw_profiles(data = abiotic_stresses$normalized_counts, 
membership = abiotic_stresses$heat_DEGs_coseq_membership, 
conds = unique(abiotic_stresses$conditions), k = 3) 

OceaneCsn/DIANE documentation built on Jan. 10, 2024, 6:43 p.m.