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)