Smooth gene expression, used primarily within conos::correctGenes. Used to smooth gene expression values in order to better represent the graph structure. Use diffusion of expression on graph with the equation dv = exp(-a * (v + b))
smooth_count_matrix(
edge_verts,
edge_weights,
count_matrix,
is_label_fixed,
max_n_iters = 10L,
diffusion_fading = 1,
diffusion_fading_const = 0.1,
tol = 0.001,
verbose = TRUE,
normalize = FALSE
)
edge vertices of igraph graph object
edge weights of igraph graph object
gene count matrix
boolean Whether label is fixed
integer Maximal number of iterations (default=10)
numeric Constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=1.0)
numeric Another constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=0.1)
numeric Absolute tolerance as a stopping criteria (default=1e-3)
boolean Verbose mode (default=TRUE)
boolean Whether to normalize values (default=FALSE)
matrix from input graph, with labels propagated