v1.2.6 - New version

Russel88 · Sep 7, 2022 · fb65148 · fb65148
1 parent c507694
commit fb65148
Show file tree

Hide file tree

Showing 15 changed files with 148 additions and 46 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RCon3D
 Title: Analysis of Confocal Images of Microbial Biofilms
-Version: 1.2.5
+Version: 1.2.6
 Authors@R: person("Jakob", "Russel", email = "russel2620@gmail.com", role = c("aut", "cre"))
 Description: Various 3D analyses of confocal images. E.g. Quantification, co-aggregation and identifying 3D aggregates.
 Depends: R (>= 3.2.5)
@@ -21,4 +21,4 @@ Suggests:
 License: GPL (>= 3) | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.1
diff --git a/R/quant.R b/R/quant.R
@@ -1,16 +1,17 @@
 #' Quantifies the pixels in images
 #'
-#' Quantifies the number of pixels for each channel in each layer (z-stack)
+#' Quantifies the number of pixels for each channel in any direction (default z-stack)
 #' @param imgs The paths of array files; i.e. output from \code{loadIMG} or \code{findIMG} functions.
 #' @param channels Character vector with name(s) of channels. Channel names should be in the names of the array files
 #' @param naming Optional. Add metadata to the output dataframe by looking through names of array files. Should be a list of character vectors, each list element will be added as a variable. Example: naming=list(Time=c("T0","T1","T2")). The function inserts a variable called Time, and then looks through the names of the array files and inserts characters mathcing either T0, T1 or T2
 #' @param cores Number of cores for parallel computing
+#' @param axis Axis to aggregate over (1: x, 2: y, 3:z). Default 3 (z-axis)
 #' @keywords array image quantify
 #' @return A dataframe with number of pixels for each layer
 #' @import foreach doSNOW
 #' @export
 
-quant <- function(imgs,channels,naming = NULL,cores = 1) {
+quant <- function(imgs,channels,naming = NULL,cores = 1,axis=3) {
 
   # Loop for each channel
   qua.fin <- list()
@@ -41,7 +42,7 @@ quant <- function(imgs,channels,naming = NULL,cores = 1) {
       ch_t <- readRDS(ch_files[k])
 
       # Count for each layer
-      q <- apply(ch_t, 3, sum)
+      q <- apply(ch_t, axis, sum)
 
       # Output
       temp <- cbind(sub(paste0("_Array.*"),"",sub(".*/", "", ch_files[k])),channels[z],q,1:length(q))

diff --git a/man/clumps.Rd b/man/clumps.Rd
diff --git a/man/clumps_dist.Rd b/man/clumps_dist.Rd
diff --git a/man/clumps_plot.Rd b/man/clumps_plot.Rd
diff --git a/man/co_agg.Rd b/man/co_agg.Rd
diff --git a/man/cross_ratio.Rd b/man/cross_ratio.Rd
diff --git a/man/layer_split.Rd b/man/layer_split.Rd
diff --git a/man/loadIMG.Rd b/man/loadIMG.Rd
diff --git a/man/morphIMG.Rd b/man/morphIMG.Rd
diff --git a/man/occupancy.Rd b/man/occupancy.Rd
diff --git a/man/quant.Rd b/man/quant.Rd
diff --git a/man/smoothIMG.Rd b/man/smoothIMG.Rd
diff --git a/man/threshIMG.Rd b/man/threshIMG.Rd
diff --git a/man/xy_splits.Rd b/man/xy_splits.Rd