diff --git a/NAMESPACE b/NAMESPACE index 64f735fd8..21f2eb81c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -11,6 +11,7 @@ export(addGenesPerc) export(addGiottoImage) export(addGiottoImageToSpatPlot) export(addHMRF) +export(addHMRF_V2) export(addNetworkLayout) export(addStatistics) export(adjustGiottoMatrix) @@ -75,6 +76,7 @@ export(dimPlot) export(dimPlot2D) export(dimPlot3D) export(doHMRF) +export(doHMRF_V2) export(doHclust) export(doKmeans) export(doLeidenCluster) @@ -95,6 +97,7 @@ export(filterDistributions) export(filterGiotto) export(filterICG) export(filterInteractionChangedGenes) +export(filterSpatialGenes) export(findCPG) export(findCellProximityGenes) export(findGiniMarkers) @@ -182,6 +185,7 @@ export(runSpatialDeconv) export(runSpatialEnrich) export(runUMAP) export(runtSNE) +export(sampling_sp_genes) export(screePlot) export(selectPatternGenes) export(showClusterDendrogram) diff --git a/man/initHMRF_V2.Rd b/man/initHMRF_V2.Rd index 305368082..7565ba70f 100644 --- a/man/initHMRF_V2.Rd +++ b/man/initHMRF_V2.Rd @@ -76,6 +76,5 @@ Second, the filtered gene set is subject to sampling to select 500 Third, once spatial genes are finalized, we are ready to initialize HMRF. This consists of running a K-means algorithm to determine initial centroids (nstart, hmrf_seed) of HMRF. The initialization is then finished. - This function returns a list containing y (expression), nei (neighborhood structure), numnei (number of neighbors), blocks (graph colors), damp (dampened factor), mu (mean), sigma (covariance), k, genes, edgelist. This information is needed for the second step, doHMRF. } diff --git a/src/RcppExports.o b/src/RcppExports.o new file mode 100644 index 000000000..29c590d2a Binary files /dev/null and b/src/RcppExports.o differ diff --git a/src/processing.o b/src/processing.o new file mode 100644 index 000000000..d0cea90af Binary files /dev/null and b/src/processing.o differ