- corrected formatting bug in documentation of channelSummaryStats.Rd()

- corrected bug in channelSummaryStats (when channels are not explicitly provided)
- bumped version to 0.99.8

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CytoMDS
 Title: Low Dimensions projection of cytometry samples
-Version: 0.99.7
+Version: 0.99.8
 Authors@R:
     c(person(given = "Philippe",
              family = "Hauchamps",

NEWS.md

@@ -45,6 +45,8 @@ for not loading the whole flowSet in memory at once.
 unidimensional histograms and store them instead of recalculating them each
 time a distance between 2 samples is calculated. This improves CPU time and
 memory consumption.
+
+### CytoMDS 0.99.8
 - renamed `getChannelSummaryStats()` into `channelSummaryStats()`
 - in `channelSummaryStats(), added support for `BiocParallel`, and allowed
 for not loading the whole flowSet in memory at once.

R/stats.R

@@ -1106,6 +1106,10 @@ pairwiseEMDDist <- function(
             packages = c("flowCore"))) {
     #browser()
 
+    if (!is.numeric(nSamples) || nSamples < 1) {
+        stop("nSamples should be a numeric >= 1")
+    }
+
     nStats <- length(statFUNs)
     if (nStats < 1) {
         stop("At least one stat function should be provided for calculation")
@@ -1241,7 +1245,7 @@ pairwiseEMDDist <- function(
 
     # rearrange outputs
 
-    nCh <- length(channels)
+    nCh <- ncol(statMatBlockList[[1]][[1]])
     chStats <- list()
     for (s in seq_along(statFUNs)){
         chStats[[s]] <- matrix(
@@ -1266,8 +1270,9 @@ pairwiseEMDDist <- function(
     chStats
 }
 
-#' @title Calculate a summary statistic of some channels of 
-#' all flowFrames of a flowSet 
+#' @title Summary statistics per channel computation
+#' @description Computation of summary statistic for selected channels,
+#' for all flowFrames of a flowSet.   
 #' This method provides two different input modes:
 #' - the user provides directly a flowSet loaded in memory (RAM).
 #' - the user provides (1.) a number of samples `nSamples`; (2.) an ad-hoc 
@@ -1377,6 +1382,9 @@ channelSummaryStats <- function(
             return(fs[[ffIndex]])
         }
         nSamples <- length(x)
+        if (nSamples < 1) {
+            stop("empty flowSet passed")
+        }
         chStats <- .channelSummaryStats(
             nSamples = nSamples,
             loadFlowFrameFUN = getFF,

tests/testthat/test-stats.R

@@ -617,7 +617,7 @@ test_that("channelSummaryStats works", {
         fsAll,
         channels = channelsOrMarkers,
         statFUNs = list("mean" = mean, "std.dev" = stats::sd),
-        verbose = TRUE)
+        verbose = FALSE)
 
     expect_equal(names(ret), c("mean", "std.dev"))
     expect_equal(unname(rownames(ret[[1]])), flowCore::sampleNames(fsAll))
@@ -676,6 +676,31 @@ test_that("channelSummaryStats works", {
     expect_equal(unname(ret[1,1]), 1.900298)
     expect_equal(unname(ret[1,2]), 1.39186533)
     expect_equal(unname(ret[1,3]), 1.8544648)
+
+    # case where no channels is provided
+    ret <- channelSummaryStats(
+        fsAll,
+        statFUNs = list("mean" = mean, "std.dev" = stats::sd),
+        verbose = FALSE
+    )
+
+    allSignalChannels <- 
+        flowCore::colnames(fsAll)[CytoPipeline::areSignalCols(fsAll)]
+    nSignalCh <- length(allSignalChannels)
+
+    allSignalChannelNames <- allSignalChannels
+    for (i in seq_along(allSignalChannels)) {
+        channelMarker <- 
+            flowCore::getChannelMarker(fsAll[[1]], allSignalChannels[i])$desc
+        if (!is.null(channelMarker) && !is.na(channelMarker)){
+            allSignalChannelNames[i] <- channelMarker
+        }
+    }
+
+    expect_equal(unname(rownames(ret[[1]])), 
+                 c("Donor1", "Donor2", "Agg1", "Agg2", "Agg3"))
+    expect_equal(unname(colnames(ret[[1]])), allSignalChannelNames)
+
 })
 
 test_that("channelSummaryStats dynamic memory loading simulation", {
@@ -690,7 +715,7 @@ test_that("channelSummaryStats dynamic memory loading simulation", {
     channelsOrMarkers <- c("FSC-A", "SSC-A", "BV785 - CD3")
 
     nSamples <- 10
-    verbose <- TRUE
+    verbose <- FALSE
     ret <- CytoMDS::channelSummaryStats(
         x = nSamples,
         loadFlowFrameFUN = simulMemoryLoad,