diff --git a/NAMESPACE b/NAMESPACE index 2b24a8182..437f5c8ef 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -16,7 +16,6 @@ S3method(seurat_meta,seurat) S3method(seurat_ref,Seurat) S3method(seurat_ref,seurat) export(average_clusters) -export(average_clusters_filter) export(binarize_expr) export(calculate_pathway_gsea) export(call_consensus) @@ -38,7 +37,6 @@ export(gene_pct_markerm) export(get_vargenes) export(gmt_to_list) export(insert_meta_object) -export(make_comb_ref) export(marker_select) export(matrixize_markers) export(object_ref) @@ -46,7 +44,6 @@ export(overcluster) export(overcluster_test) export(parse_loc_object) export(plot_best_call) -export(plot_cols) export(plot_cor) export(plot_cor_heatmap) export(plot_dims) diff --git a/R/compute_similarity.R.REMOVED.git-id b/R/compute_similarity.R.REMOVED.git-id index 3a97efb20..9419e14e2 100644 --- a/R/compute_similarity.R.REMOVED.git-id +++ b/R/compute_similarity.R.REMOVED.git-id @@ -1 +1 @@ -e158bc0a2e5ca6c5a584e9ccb87a6a96ec91ffc4 \ No newline at end of file +a47e09e0d25dac5310ae44a3351c100c21edd6ae \ No newline at end of file diff --git a/R/plot.R.REMOVED.git-id b/R/plot.R.REMOVED.git-id index e75ac43bd..1ceedbc76 100644 --- a/R/plot.R.REMOVED.git-id +++ b/R/plot.R.REMOVED.git-id @@ -1 +1 @@ -97529b93e40b878045d2e11284532e37db8fa8fc \ No newline at end of file +f70b7643b940cce1061d7f6cc5a350019c25e29f \ No newline at end of file diff --git a/R/utils.R.REMOVED.git-id b/R/utils.R.REMOVED.git-id index c8bc998b0..a27dce281 100644 --- a/R/utils.R.REMOVED.git-id +++ b/R/utils.R.REMOVED.git-id @@ -1 +1 @@ -e33a670c61e5453863d95a6478818138bb28d0c6 \ No newline at end of file +2c37236168b5691258c64d82367c72a85d96eae3 \ No newline at end of file diff --git a/man/RowVar.Rd b/man/RowVar.Rd deleted file mode 100644 index e520d4850..000000000 --- a/man/RowVar.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{RowVar} -\alias{RowVar} -\title{get var per row for matrix} -\usage{ -RowVar(x, na.rm = TRUE) -} -\arguments{ -\item{x}{expression matrix} - -\item{na.rm}{logical. -Should missing values (including NaN) be omitted from the calculations?} -} -\value{ -vector of numeric values -} -\description{ -get var per row for matrix -} diff --git a/man/average_clusters_filter.Rd b/man/average_clusters_filter.Rd deleted file mode 100644 index d43d58707..000000000 --- a/man/average_clusters_filter.Rd +++ /dev/null @@ -1,54 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{average_clusters_filter} -\alias{average_clusters_filter} -\title{Average expression values per cluster, filtered by set parameter, -defaults to calculating background} -\usage{ -average_clusters_filter( - mat, - metadata, - if_log = TRUE, - filter_on = "nGene", - group_by = NULL, - filter_method = "<=", - filter_value = 300 -) -} -\arguments{ -\item{mat}{expression matrix} - -\item{metadata}{data.frame or vector containing -cluster assignments per cell, and attribute to filter on. -Order must match column order in supplied matrix. If a data.frame -provide the cluster_col parameters.} - -\item{if_log}{input data is natural log, -averaging will be done on unlogged data} - -\item{filter_on}{column in metadata to filter on} - -\item{group_by}{column name to use for cluster identity} - -\item{filter_method}{"<", "==", ">" compared to filter_value} - -\item{filter_value}{baseline minimum as background cutoff} -} -\value{ -average expression matrix, with genes for row names, -and clusters for column names -} -\description{ -Average expression values per cluster, filtered by set parameter, -defaults to calculating background -} -\examples{ -average_clusters_filter( - mat = pbmc_matrix_small, - metadata = pbmc_meta, - group_by = "classified", - filter_on = "seurat_clusters", - filter_method = "==", - filter_value = "1" -) -} diff --git a/man/clustify_intra.Rd b/man/clustify_intra.Rd deleted file mode 100644 index a1b6aa519..000000000 --- a/man/clustify_intra.Rd +++ /dev/null @@ -1,51 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{clustify_intra} -\alias{clustify_intra} -\title{Intra-experiment cluster projection for one sample/set to the rest} -\usage{ -clustify_intra( - expr_mat, - metadata, - query_genes, - cluster_col, - sample_col, - sample_id, - per_cell = FALSE, - compute_method = "spearman", - ... -) -} -\arguments{ -\item{expr_mat}{single-cell expression matrix or Seurat object} - -\item{metadata}{cell cluster assignments, supplied as a -vector or data.frame. If data.frame is supplied then \code{cluster_col} -needs to be set. Not required if running correlation per cell.} - -\item{query_genes}{A vector of genes of interest to compare. If NULL, -then common genes between -the expr_mat and ref_mat will be used for comparision.} - -\item{cluster_col}{column in metadata that contains cluster ids per cell. -Will default to first -column of metadata if not supplied. Not required if -running correlation per cell.} - -\item{sample_col}{column in metadata that contains sample/subset info} - -\item{sample_id}{ids in column to serve as reference} - -\item{per_cell}{if true run per cell, otherwise per cluster.} - -\item{compute_method}{method(s) for computing similarity scores} - -\item{...}{additional arguments to pass to compute_method function} -} -\value{ -matrix of correlation values, clusters as row names -and column names -} -\description{ -Intra-experiment cluster projection for one sample/set to the rest -} diff --git a/man/compute_mean_expr.Rd b/man/compute_mean_expr.Rd deleted file mode 100644 index 7c9f50c7d..000000000 --- a/man/compute_mean_expr.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/compute_similarity.R -\name{compute_mean_expr} -\alias{compute_mean_expr} -\title{compute mean of clusters} -\usage{ -compute_mean_expr(expr_mat, sc_assign, sc_clust) -} -\arguments{ -\item{expr_mat}{matrix of gene expression} - -\item{sc_assign}{vector of cluster assignments} - -\item{sc_clust}{unique vector of cluster assignments} -} -\value{ -matrix of average expression per cluster -} -\description{ -compute mean of clusters -} diff --git a/man/make_comb_ref.Rd b/man/make_comb_ref.Rd deleted file mode 100644 index 281788079..000000000 --- a/man/make_comb_ref.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{make_comb_ref} -\alias{make_comb_ref} -\title{make combination ref matrix to assess intermixing} -\usage{ -make_comb_ref(ref_mat, if_log = TRUE, sep = "_and_") -} -\arguments{ -\item{ref_mat}{reference expression matrix} - -\item{if_log}{whether input data is natural} - -\item{sep}{separator for name combinations} -} -\value{ -expression matrix -} -\description{ -make combination ref matrix to assess intermixing -} -\examples{ -ref <- make_comb_ref( - cbmc_ref, - sep = "_+_" -) -ref[1:3, 1:3] -} diff --git a/man/plot_cols.Rd b/man/plot_cols.Rd deleted file mode 100644 index 75ec46c25..000000000 --- a/man/plot_cols.Rd +++ /dev/null @@ -1,50 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/plot.R -\name{plot_cols} -\alias{plot_cols} -\title{Plot variable median per cluster from reference metadata -vs new assigned metadata, for visually evaluating classification} -\usage{ -plot_cols( - metadata, - cluster_col, - cluster_col_called, - plot_col, - metadata_ref, - cluster_col_ref, - plot_col_ref -) -} -\arguments{ -\item{metadata}{clustify-ed metadata} - -\item{cluster_col}{metadata column for original clustering} - -\item{cluster_col_called}{metadata column for clustifyr assignments} - -\item{plot_col}{metadata column to plot} - -\item{metadata_ref}{reference single cell RNA seq metadata} - -\item{cluster_col_ref}{metadata column for cluster for reference} - -\item{plot_col_ref}{metadata column to plot for reference} -} -\value{ -ggplot scatterplot -} -\description{ -Plot variable median per cluster from reference metadata -vs new assigned metadata, for visually evaluating classification -} -\examples{ -plot_cols( - metadata = pbmc_meta, - cluster_col = "seurat_clusters", - cluster_col_called = "classified", - plot_col = "UMAP_1", - metadata_ref = pbmc_meta, - cluster_col_ref = "classified", - plot_col_ref = "UMAP_1" -) -} diff --git a/tests/testthat/test_plots.R.REMOVED.git-id b/tests/testthat/test_plots.R.REMOVED.git-id index 637ce4c66..865ea85d0 100644 --- a/tests/testthat/test_plots.R.REMOVED.git-id +++ b/tests/testthat/test_plots.R.REMOVED.git-id @@ -1 +1 @@ -5b199a209843244996482773e965af1738f030b5 \ No newline at end of file +7c739658e323fd24491749f1f26dbcdc832b7075 \ No newline at end of file diff --git a/tests/testthat/test_utils.R.REMOVED.git-id b/tests/testthat/test_utils.R.REMOVED.git-id index 9c168c83b..5dad3858f 100644 --- a/tests/testthat/test_utils.R.REMOVED.git-id +++ b/tests/testthat/test_utils.R.REMOVED.git-id @@ -1 +1 @@ -0a1373125ad8ffe79f54cb0a0ee7cee9c33adde7 \ No newline at end of file +5ec1b9ac2ffeccd1b5f3c7de7403047fd2b83e10 \ No newline at end of file