S7 compartmap objects for analysis

DESCRIPTION

@@ -42,7 +42,9 @@ Imports:
    DelayedMatrixStats,
    Matrix,
    RMTstat,
-   impute
+   impute,
+   data.table,
+   S7
 Suggests:
    csaw,
    minfi,

NAMESPACE

@@ -1,16 +1,30 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[","compartmap::CompartmentCall")
+S3method("[","compartmap::MultiCompartmentCall")
+S3method(plot,"compartmap::CompartmentCall")
+S3method(plot,"compartmap::MultiCompartmentCall")
+export(CompartmapCall)
+export(CompartmentCall)
+export(DF)
+export(MultiCompartmentCall)
+export(SingleCellCompartmentCall)
+export(agr)
+export(agreement)
 export(agrestiCoullCI)
 export(bootstrapCompartments)
 export(condenseRE)
 export(condenseSE)
+export(corr)
 export(estRMT)
 export(extractOpenClosed)
 export(fexpit)
+export(fill_missing)
 export(filterCompartments)
 export(filterOpenSea)
 export(fisherZ)
 export(fixCompartments)
+export(flip)
 export(flogit)
 export(getABSignal)
 export(getATACABsignal)
@@ -28,27 +42,33 @@ export(getOpenSeas)
 export(getSVD)
 export(getSeqLengths)
 export(getShrinkageTargets)
+export(get_name)
 export(hdf5TFIDF)
 export(ifisherZ)
 export(importBigWig)
 export(imputeKNN)
+export(is_unitarized)
 export(meanSmoother)
 export(plotAB)
 export(plotCorMatrix)
 export(precomputeBootstrapMeans)
 export(preprocessArrays)
 export(removeEmptyBoots)
+export(resolution)
 export(scCompartments)
 export(shrinkBins)
 export(sparseToDenseMatrix)
+export(subset_chr)
 export(summarizeBootstraps)
 export(transformTFIDF)
+export(unitarize)
 import(DelayedArray)
 import(DelayedMatrixStats)
 import(GenomicRanges)
 import(HDF5Array)
 import(Matrix)
 import(RaggedExperiment)
+import(S7)
 import(SummarizedExperiment)
 importFrom(BiocSingular,IrlbaParam)
 importFrom(BiocSingular,runSVD)
@@ -60,17 +80,30 @@ importFrom(GenomeInfoDb,seqlengths)
 importFrom(GenomeInfoDb,seqlevels)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
+importFrom(data.table,":=")
+importFrom(data.table,.I)
+importFrom(data.table,.N)
+importFrom(data.table,as.data.table)
+importFrom(data.table,data.table)
+importFrom(data.table,dcast)
+importFrom(data.table,melt)
+importFrom(data.table,rbindlist)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_raster)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,scale_fill_gradient2)
+importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
 importFrom(graphics,abline)
 importFrom(graphics,barplot)
 importFrom(graphics,par)
 importFrom(methods,as)
+importFrom(methods,initialize)
 importFrom(methods,is)
 importFrom(parallel,mclapply)
 importFrom(rlang,.data)
@@ -80,4 +113,5 @@ importFrom(stats,median)
 importFrom(stats,optim)
 importFrom(stats,sd)
 importFrom(stats,weighted.mean)
+importFrom(utils,combn)
 importFrom(utils,data)

R/analysis.R

@@ -0,0 +1,26 @@
+#' Compute sign agreement of a matrix of singular values
+#' @param mat A matrix of compartment calls where each column is a single-cell
+#' or grouped set of singular values
+#' @importFrom utils combn
+#' @export
+agreement <- function(mat) {
+  cmbs <- combn(1:ncol(mat), 2)
+  ncols <- ncol(mat)
+  agrmat <- matrix(nrow = ncols, ncol = ncols)
+  for (cidx in seq(ncol(cmbs))) {
+    i <- cmbs[, cidx][1]
+    j <- cmbs[, cidx][2]
+    res <- .agreement(mat[, i], mat[, j])
+    agrmat[i, j] <- res
+    agrmat[j, i] <- res
+  }
+  dimnames(agrmat) <- list(colnames(mat), colnames(mat))
+  diag(agrmat) <- 1
+  agrmat
+}
+
+.agreement <- function(v1, v2) {
+  b1 <- v1 > 0
+  b2 <- v2 > 0
+  sum(b1 == b2) / length(v1)
+}