Draw expression profiles of a clustering

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)