###
### NAMESPACE
###
import(methods)
import(Thresher)

## Hack around bug in R-devel (4.1) that does weird things with a
## downstream Suggested package and an onLoad funciton.
importFrom("flexmix", "flexmix")
importFrom("KernSmooth", "bkde2D") # called without import by' smoothScatter' through 'grDevices'

importFrom("stats", "dist", "hclust", "cmdscale", "as.dist",
           "rbinom", "as.dendrogram", "as.hclust", "quantile",
           "cutree")
importFrom("utils", "data")
importFrom("graphics", "par", "barplot", "smoothScatter")
importFrom("grDevices", "dev.interactive", "devAskNewPage", "topo.colors")
importFrom("cluster", "pam", "silhouette")
importFrom("Rtsne", "Rtsne")
importFrom("ClassDiscovery", "plotColoredClusters")
importMethodsFrom("ClassDiscovery", "hist")
importFrom("Polychrome", "dark.colors")
importFrom("dendextend", "prune")
importFrom("igraph", "vertex_attr", "set_vertex_attr",
           "layout_nicely", "graph_from_data_frame")
importFrom("umap", "umap")
importFrom("kohonen", "som", "somgrid")

# 01-metrics
export("binaryDistance")

# 02-binaryMatrix
exportClasses("BinaryMatrix")
export("BinaryMatrix", "removeDuplicateFeatures", "removeDuplicates")

exportMethods("[", "dim", "summary", "t", "print", "show")

# 03-thresh
exportClasses("ThreshedBinaryMatrix")
export("threshLGF")

# 04-vis
exportClasses("Mercator")
export("Mercator", "addVisualization", "getClusters", "recluster")

exportMethods("hist", "plot", "barplot", "scatter")

export(setClusters, recolor, remapColors)

# 05-graph
export(downsample)

