Merge pull request #139 from cnio-bu/rc2_2

Update beyondcell to version 2.2.0

.github/workflows/conda_build.yml

@@ -64,11 +64,11 @@ jobs:
       - name: Archive beyondcell package for GNU/Linux
         uses: actions/upload-artifact@v3
         with:
-          name: Linux_r-beyondcell-v2.1.0
-          path: /usr/share/miniconda3/envs/bc_builds/conda-bld/linux-64/r-beyondcell-2.1.0-r42_0.tar.bz2
+          name: Linux_r-beyondcell-v2.2.0
+          path: /usr/share/miniconda3/envs/bc_builds/conda-bld/linux-64/r-beyondcell-2.2.0-r43_0.tar.bz2
 
       - name: Archive beyondcell package for macOS
         uses: actions/upload-artifact@v3
         with:
-          name: macOS_r-beyondcell-v2.1.0
-          path: /Users/runner/miniconda3/envs/bc_builds/conda-bld/osx-64/r-beyondcell-2.1.0-r42_0.tar.bz2
+          name: macOS_r-beyondcell-v2.2.0
+          path: /Users/runner/miniconda3/envs/bc_builds/conda-bld/osx-64/r-beyondcell-2.2.0-r43_0.tar.bz2

.github/workflows/helpers/mambabuild.yml

@@ -6,4 +6,6 @@ channels:
   - defaults
 
 dependencies:
-  - boa=0.6.2
+  - boa
+
+channel_priority: strict

.github/workflows/r-beyondcell/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = '2.1.0' %}
+{% set version = '2.2.0' %}
 {% set name = "beyondcell" %}
 {% set posix = 'm2-' if win else '' %}
 {% set native = 'm2w64-' if win else '' %}

CHANGELOG.md

@@ -1,6 +1,13 @@
+# [2.2.0] - 2023-07-06
+* **Fixed** an issue ([#132](https://github.com/cnio-bu/beyondcell/issues/132)) where `bcScore`'s check for normalized data failed.
+* **Fixed** an issue ([#135](https://github.com/cnio-bu/beyondcell/issues/135)) where `bcRanks` was not computing the residual's mean.
+* **Updated** tutorials.
+* **Removed** `bcRanks` "general" statistics computation.
+* **Removed** `GetStatistics` function.
+
 # [2.1.0] - 2023-03-31
-* **Fixed** error in `bcClusters` and `bcSignatures` when `spatial = TRUE` and `images = NULL`.
-* **Fixed** title error in `bc4Squares`. The curent title matches the corresponding `idents` level.
+* **Fixed** an error in `bcClusters` and `bcSignatures` when `spatial = TRUE` and `images = NULL`.
+* **Fixed** title error in `bc4Squares`. The current title matches the corresponding `idents` level.
 * **Fixed** error in `bc4Squares` when drug names were passed as `topnames`.
 * **Updated** pre-loaded collections, which have been trimmed to 250 up and 250 down genes.
 * **Updated** SSc collection, which only contains protein-coding genes.
@@ -22,17 +29,17 @@
 * **Removed** the `method` argument from `bcUMAP`. Only the UWOT library implementation of UMAP is available.
 
 # [1.3.3] - 2022-01-12
-* **Fixed** an error in `bcSubset` when filtering by the proportion of `NaN` values. Previously, the beyondcell object wasn't subset when using `nan.sigs` or `nan.cells`. Now those signatures/cells below or equal to the `NaN` threshold are kept. Related to issue #21.
+* **Fixed** an error in `bcSubset` when filtering by the proportion of `NaN` values. Previously, the beyondcell object wasn't a subset when using `nan.sigs` or `nan.cells`. Now those signatures/cells below or equal to the `NaN` threshold are kept. Related to issue #21.
 
 # [1.3.2] - 2021-12-20
-* **Fixed** an issue (#17) where if all the cells have a number of expressed genes < `expr.thres`, 
+* **Fixed** an issue ([#17](https://github.com/cnio-bu/beyondcell/issues/17)) where if all the cells have a number of expressed genes < `expr.thres`, 
 all the values for that signature will be `NaN` and so will be the switch point. 
 
 # [1.3.1] - 2021-09-9
 * **Added** group annotation to rank tables: high/low/differential sensitivity is now defined for each tested drug.
 
 # [1.2.1] - 2021-06-29
-* **Fixed** an issue (#14) where `bcSignatures` would fail when used with pathways
+* **Fixed** an issue ([#14](https://github.com/cnio-bu/beyondcell/issues/14)) where `bcSignatures` would fail when used with pathways
 
 # [1.2.0] - 2021-06-8
 * **Fixed** an issue where `bcMerge` would fail if the background matrix was empty. 

DESCRIPTION

@@ -2,7 +2,7 @@ Type: Package
 Package: beyondcell
 Title: A Tool for the Analysis of Tumour Therapeutic Heterogeneity in
     single-cell RNA-seq and Spatial Transcriptomics
-Version: 2.1.0
+Version: 2.2.0
 Authors@R: c(
     person("Maria Jose", "Jimenez-Santos", , "[email protected]", role = c("aut", "cre")),
     person("Santiago", "Garcia-Martin", , "[email protected]", role = "aut"),

NAMESPACE

@@ -7,7 +7,6 @@ export(FindDrugs)
 export(GenerateGenesets)
 export(GetCollection)
 export(GetIDs)
-export(GetStatistics)
 export(ListFilters)
 export(Mean.Med.SD)
 export(SwitchPoint)
@@ -34,9 +33,11 @@ import(Seurat)
 import(ggplot2)
 import(scales)
 import(stringr)
+import(tidyverse)
 importFrom(DMwR,knnImputation)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(cowplot,theme_cowplot)
+importFrom(data.table,frank)
 importFrom(dplyr,left_join)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,colorRampPalette)

R/Basics.R

@@ -82,165 +82,6 @@ Mean.Med.SD <- function(x) {
                   c("mean", "median", "sd")))
 }
 
-#' @title Computes the BCS' statistics and ranks
-#' @description This function computes the beyondcell scores' (BCS) statistics
-#' and ranks returned by \code{\link[beyondcell]{bcRanks}}.
-#' @name GetStatistics
-#' @param bc \code{\link[beyondcell]{beyondcell}} object.
-#' @param signatures Vector with the names of the signatures of interest.
-#' @param cells Vector with the names of the cells of interest.
-#' @param pb \code{\link[utils]{txtProgressBar}}.
-#' @param total Number of iterations to complete the \code{pb}.
-#' @param i Iteration number. Used to increase the \code{pb}.
-#' @param n.rows Number of signatures. Used to increase the \code{pb}.
-#' @param extended If \code{extended = TRUE}, this function returns the switch
-#' point, mean, median, sd, variance, min, max, proportion of \code{NaN} and
-#' residuals' mean per signature. If \code{extended = FALSE}, this function
-#' returns only the switch point, mean and residuals' mean.
-#'
-#' @return A \code{data.frame} with the BCS' statistics and ranks.
-#' @examples
-#' @export
-
-GetStatistics <- function(bc, signatures, cells, pb, total, i, n.rows,
-                          extended) {
-  # --- Checks ---
-  # Check that bc is a beyondcell object.
-  if (class(bc) != "beyondcell") stop('bc must be a beyondcell object.')
-  # Check signatures.
-  in.signatures <- !is.null(signatures) & signatures %in% rownames(bc@normalized)
-  if (all(!in.signatures)) {
-    stop('None of the specified signatures were found.')
-  } else if (any(!in.signatures)) {
-    warning(paste0('These signatures were not found in bc: ',
-                   paste0(signatures[!in.signatures], collapse = ", "), '.'))
-  }
-  # Check cells.
-  in.cells <- !is.null(cells) & cells %in% colnames(bc@normalized)
-  if (all(!in.cells)) {
-    stop('None of the specified cells were found.')
-  } else if (any(!in.cells)) {
-    warning(paste0('These cells were not found in bc: ',
-                   paste0(cells[!in.cells], collapse = ", "), '.'))
-  }
-  # Check pb.
-  if (class(pb) != "txtProgressBar") stop('pb must be a txtProgressBar object.')
-  # Check total.
-  if (length(total) != 1 | total[1] <= 0 | total[1]%%1 != 0) {
-    stop('total must be a positive integer.')
-  }
-  # Check i.
-  if (length(i) != 1 | i[1] <= 0 | i[1]%%1 != 0) {
-    stop('i must be a positive integer.')
-  }
-  # Check n.rows.
-  if (length(n.rows) != 1 | n.rows[1] <= 0 | n.rows[1]%%1 != 0) {
-    stop('n.rows must be a positive integer.')
-  }
-  # Check extended.
-  if (length(extended) != 1 | !is.logical(extended[1])) {
-    stop('extended must be TRUE or FALSE.')
-  }
-  # --- Code ---
-  # Signatures and cells.
-  signatures <- signatures[in.signatures]
-  cells <- cells[in.cells]
-  # Bins: Number of iterations to complete each 1% of the progress bar.
-  bins <- ceiling(total / 100)
-  # Switch points per signature.
-  switch.p <- bc@switch.point[signatures]
-  if (extended) {
-    # Dataframe with mean, median and sd per signature.
-    data <- cbind(seq_len(n.rows) + (n.rows * 6) * (i - 1),
-                  bc@normalized[signatures, cells])
-    mean.med.sd <- as.data.frame(t(apply(data, 1, function(u) {
-      mms <- round(Mean.Med.SD(u[-1]), digits = 2)
-      ### Update the progress bar.
-      if (u[1]%%bins == 0) {
-        Sys.sleep(0.1)
-        setTxtProgressBar(pb, value = u[1])
-      }
-      return(mms)
-    })))
-    # Variance per signature.
-    data[, 1] <- data[, 1] + n.rows
-    variance.bcscore <- apply(data, 1, function(v) {
-      variance <- var(v[-1], na.rm = TRUE)
-      ### Update the progress bar.
-      if (v[1]%%bins == 0) {
-        Sys.sleep(0.1)
-        setTxtProgressBar(pb, value = v[1])
-      }
-      return(variance)
-    })
-    # Min normalized BCS per signature.
-    data[, 1] <- data[, 1] + n.rows
-    min.bcscore <- apply(data, 1, function(w) {
-      min.bcs <- min(w[-1], na.rm = TRUE)
-      ### Update the progress bar.
-      if (w[1]%%bins == 0) {
-        Sys.sleep(0.1)
-        setTxtProgressBar(pb, value = w[1])
-      }
-      return(min.bcs)
-    })
-    # Max normalized BCS per signature.
-    data[, 1] <- data[, 1] + n.rows
-    max.bcscore <- apply(data, 1, function(x) {
-      max.bcs <- max(x[-1], na.rm = TRUE)
-      ### Update the progress bar.
-      if (x[1]%%bins == 0) {
-        Sys.sleep(0.1)
-        setTxtProgressBar(pb, value = x[1])
-      }
-      return(max.bcs)
-    })
-    # NA proportion per signature.
-    data[, 1] <- data[, 1] + n.rows
-    prop.na <- apply(data, 1, function(y) {
-      nas <- round(sum(is.na(y[-1]))/length(y[-1]), digits = 2)
-      ### Update the progress bar.
-      if (y[1]%%bins == 0) {
-        Sys.sleep(0.1)
-        setTxtProgressBar(pb, value = y[1])
-      }
-      return(nas)
-    })
-    # Residuals.
-    normalized <- cbind(seq_len(n.rows) + (n.rows * i * 5) + (n.rows * (i - 1)),
-                        bc@normalized[signatures, cells])
-    # Create dataframe.
-    stats <- data.frame(switch.point = switch.p, mean = mean.med.sd$mean,
-                        median = mean.med.sd$median, sd = mean.med.sd$sd,
-                        variance = variance.bcscore, min = min.bcscore,
-                        max = max.bcscore, prop.na = prop.na,
-                        row.names = signatures)
-  } else {
-    # Mean BCS per signature.
-    mean.bc <- round(rowMeans(bc@normalized[signatures, cells], na.rm = TRUE),
-                     digits = 2)
-    # Residuals.
-    normalized <- cbind(seq_len(n.rows) + (n.rows * (i - 1)),
-                        bc@normalized[signatures, cells])
-    # Create dataframe.
-    stats <- data.frame(switch.point = switch.p, mean = mean.bc,
-                        row.names = signatures)
-  }
-  # Residuals' mean.
-  resid <- apply(normalized, 1, function(z) {
-    res <- round(mean(z[-1], na.rm = TRUE), digits = 2)
-    ### Update the progress bar.
-    if (z[1]%%bins == 0 | z[1] == total) {
-      Sys.sleep(0.1)
-      setTxtProgressBar(pb, value = z[1])
-    }
-    return(res)
-  })
-  # Update dataframe.
-  stats <- cbind(stats, data.frame(residuals.mean = resid, row.names = signatures))
-  return(stats)
-}
-
 #' @title Returns the IDs that match the specified filter's values
 #' @description This function subsets \code{df} to select only the entries that
 #' match the specified \code{filter}'s \code{values} and returns the