Updated build 0.3.1 and website

Author: lorenzobonaguro

DESCRIPTION

@@ -62,7 +62,8 @@ Imports:
     rstatix,
     tidyr,
     CytoNorm,
-    corrplot
+    corrplot,
+    S4Vectors
 Remotes:
     JinmiaoChenLab/Rphenograph,
     stuchly/Rphenoannoy,

NAMESPACE

@@ -6,6 +6,7 @@ export(change_param_name)
 export(checkInput)
 export(check_IDs)
 export(clr)
+export(condor_info)
 export(condor_session_info)
 export(confusionMatrix)
 export(corr_plot_comparison)
@@ -26,6 +27,7 @@ export(marker_wilcox_test)
 export(measured_markers)
 export(merge_condor)
 export(metaclustering)
+export(order_param)
 export(plot_confusion_HM)
 export(plot_counts_barplot)
 export(plot_dim_density)

R/astir.R

@@ -10,6 +10,7 @@
 #' @param max_epochs Maximum number of epochs, for details see `Astir` documentation.
 #' @param learning_rate Learning Rate.
 #' @param initial_epochs initial epochs, for details see `Astir` documentation.
+#' @param prefix Optional prefix for the slot name of the output.
 #' @details Predict cell types using 'Astir'. This package requires the python library `astir` and `reticulate`. This function is still experimental and was not extensively tested in cyCONDOR. In one of the next release we will document it's usage in more details on a dedicated vignette.
 #' For the moment if you want to know more feel free to reach out on our `Slack` channel. For more details on the different parameters refer to `Astir` documentation.
 #' @import reticulate
@@ -23,7 +24,7 @@ runAstir_celltype <- function(fcd,
                               max_epochs,
                               learning_rate,
                               initial_epochs,
-                              prefix = "") {
+                              prefix = NULL) {
 
   # Save the expression matrix as csv
   write.csv(x = fcd$expr[[data_slot]], file = paste0(analysis_path, "expr.csv"))
@@ -68,7 +69,7 @@ runAstir_celltype <- function(fcd,
                                         "Learning_Rate_", learning_rate,
                                         "_Initial_Epochs_", initial_epochs))
 
-  fcd[["astir"]][[paste(prefix, "Astir_cell_type", data_slot, sep = "_")]] <- df
+  fcd[["astir"]][[paste("Astir_cell_type", sub("^_", "", paste(prefix, data_slot, sep = "_")), sep = "_")]] <- df
 
   return(fcd)
 
@@ -86,6 +87,7 @@ runAstir_celltype <- function(fcd,
 #' @param max_epochs Maximum number of epochs.
 #' @param learning_rate Learning Rate.
 #' @param initial_epochs Initial Epochs.
+#' @param prefix Optional prefix for the slot name of the output.
 #' @import reticulate
 #' @importFrom utils write.csv
 #' @return runAstir_cellstates
@@ -98,7 +100,7 @@ runAstir_cellstates <- function(fcd,
                                 max_epochs,
                                 learning_rate,
                                 initial_epochs,
-                                prefix = "") {
+                                prefix = NULL) {
 
   # Save the expression matrix as csv
   write.csv(x = fcd$expr[[data_slot]], file = paste0(analysis_path, "expr.csv"))
@@ -138,7 +140,7 @@ runAstir_cellstates <- function(fcd,
                                         "Learning_Rate_", learning_rate,
                                         "_Initial_Epochs_", initial_epochs))
 
-  fcd[["astir"]][[paste(prefix, "Astir_cell_state", data_slot, sep = "_")]] <- df
+  fcd[["astir"]][[paste("Astir_cell_state", sub("^_", "", paste(prefix, data_slot, sep = "_")), sep = "_")]] <- df
 
   return(fcd)
 

R/data_load_and_transform.R

@@ -686,6 +686,8 @@ export_sce <- function(fcd = condor,
                        dir = paste0(getwd(), "/"),
                        filename = "") {
 
+  message("This function is still experimental, if you run into any issue please let us know!")
+
   # Extracting the expression data
   exp <- as.matrix(t(fcd[["expr"]][[expr_slot]]))
 

R/data_visualization.R

@@ -225,6 +225,8 @@ confusionMatrix <- function (i = NULL, j = NULL)
 #' @param cluster_slot string specifying which clustering slot to use to find variable specified in cluster_var.
 #' @param add_pseudotime Logical, if plot should be colored by pseudotime.
 #' @param pseudotime_slot string specifying pseudotime name to use for visualization.
+#' @param add_astir Logical, if plot should be colored by Astir prediction.
+#' @param astir_slot string specifying astir description name to use for visualization.
 #' @param param parameter to visualize in the plot, this can be either a continuous variable or a categorical one, the function will react differently accordingly.
 #' @param order logical if you want to order the dots in the plot, by expression for example. This can help to find small populations of positive cells. If set to FALSE, the plotting order of the cells is randomized.
 #' @param title title of the plot.

_pkgdown.yml

@@ -104,6 +104,9 @@ reference:
   - condor_session_info
   - corr_plot_comparison
   - write_fcs
+  - condor_info
+  - export_sce
+  - order_param
 
 articles:
 - title: Detailed cyCONDOR workflows
@@ -129,5 +132,5 @@ articles:
 - title: Other workflows
   desc: >
     Additional analytical workflows
-  contents: 
+  contents:
   - Workflow_merge_panels