Merge pull request #8 from lorenzobonaguro/dev

Update to version 0.1.6

Author: lorenzobonaguro

.Rhistory

@@ -1,9 +1,13 @@
 Package: cyCONDOR
 Type: Package
 Title: Flow Cytometry data analysis toolbox
-Version: 0.1.5
-Author: Lorenzo Bonaguro
-Maintainer: Lorenzo Bonaguro <lorenzobonaguro@uni-bonn.de>
+Version: 0.1.6
+Authors@R: c(
+  person(given = "Lorenzo", family = "Bonaguro", email = "lorenzo.bonaguro@dzne.de", role = c("aut", "cre")),
+  person(given = "Charlotte", family = "Kroeger", email = "charlotte.kroeger@dzne.de", role = "aut"),
+  person(given = "Sophie", family = "Mueller", email = "sophie.mueller@dzne.de", role = "aut"),
+  person(given = "Jacqueline", family = "Leidner", email = "jacqueline.leidner@dzne.de", role = "aut")
+  )
 Description: Flow cytometry analysis workflow. The aim of this project if to 
     provide an intuitive workflow for the analysis of high-dimensionality cytometry data in R.
 URL: https://github.com/lorenzobonaguro/condor
@@ -48,7 +52,13 @@ Imports:
     DelayedMatrixStats,
     cowplot,
     dplyr,
-    reticulate
+    reticulate,
+    SummarizedExperiment,
+    diffcyt,
+    ggridges,
+    rstatix,
+    tidyr,
+    CytoNorm
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Suggests: 

DESCRIPTION

@@ -1,32 +1,45 @@
 # Generated by roxygen2: do not edit by hand
 
-export(HM_differential_marker)
-export(HM_markers)
 export(PC_loadings)
-export(barplot_frequency)
-export(boxplot_and_stats)
 export(change_param_name)
+export(checkInput)
 export(check_IDs)
 export(clr)
 export(confusionMatrix)
-export(confusion_HM)
-export(densityplot_marker)
 export(df_frequency)
-export(dotplot_cyto)
 export(filter_fcd)
+export(frequency_anova_test)
+export(frequency_friedman_test)
+export(frequency_kruskal_test)
+export(frequency_t_test)
+export(frequency_wilcox_test)
+export(getTable)
 export(harmonize_PCA)
 export(harmonize_intensities)
 export(learnUMAP)
+export(marker_wilcox_test)
+export(measured_markers)
 export(merge_condor)
 export(metaclustering)
-export(nfTransform)
-export(plot_density)
-export(plot_marker)
+export(plot_confusion_HM)
+export(plot_counts_barplot)
+export(plot_dim_density)
+export(plot_dim_red)
+export(plot_frequency_barplot)
+export(plot_frequency_boxplot)
+export(plot_marker_HM)
+export(plot_marker_boxplot)
+export(plot_marker_density)
+export(plot_marker_dotplot)
+export(plot_marker_group_HM)
+export(plot_marker_ridgeplot)
+export(plot_marker_violinplot)
 export(predict_classifier)
 export(predict_labels)
-export(prepFcsFolderData)
+export(prepInputDiffcyt)
 export(prep_fcd)
 export(prep_fjw)
+export(read_data)
 export(runAstir_cellstates)
 export(runAstir_celltype)
 export(runDM)
@@ -36,33 +49,41 @@ export(runPCA_pseudobulk)
 export(runPhenograph)
 export(runPseudotime)
 export(runUMAP)
+export(run_cytonorm)
 export(runtSNE)
 export(scaleColors)
 export(subset_fcd)
 export(train_classifier_model)
+export(train_cytonorm)
 export(train_transfer_model)
-export(violinplot_marker)
+export(transform_data)
+export(used_markers)
 import(Biobase)
 import(CytoDx)
 import(CytoML)
+import(CytoNorm)
 import(DelayedMatrixStats)
+import(FlowSOM)
 import(Hmisc)
 import(RColorBrewer)
 import(Rmisc)
 import(Rphenograph)
 import(Rtsne)
 import(SingleCellExperiment)
+import(SummarizedExperiment)
 import(caret)
 import(cowplot)
 import(destiny)
 import(devtools)
+import(diffcyt)
 import(dplyr)
 import(flowCore)
 import(flowWorkspace)
 import(ggplot2)
 import(ggpubr)
 import(ggrastr)
 import(ggrepel)
+import(ggridges)
 import(ggsci)
 import(harmony)
 import(pheatmap)
@@ -71,9 +92,13 @@ import(readr)
 import(readxl)
 import(reshape2)
 import(reticulate)
+import(rstatix)
 import(slingshot)
+import(stats)
 import(stringr)
+import(tidyr)
 import(umap)
+import(uwot)
 importFrom(Matrix,sparseMatrix)
 importFrom(igraph,membership)
 importFrom(utils,packageDescription)

NAMESPACE

@@ -1,3 +1,25 @@
+# cyCONDOR 0.1.6
+
+* Reorganization of existing visualization functions including harmonization of function names and function arguments, utilization of `condor` object as main input object and addition of more extensive documentation and error messages.
+* Added visualization functions `plot_counts_barplot()`, `plot_marker_ridgeplot()` and `plot_marker_boxplot()`
+* Added `getTable()` function to generate tables of cell population counts and frequencies, as well as mean or median marker expression for all cell population - sample - marker combinations.
+* `boxplot_and_stats()` function was replaces by `plot_frequency_boxplot()` function for visualization and several functions to conduct statistical tests on population frequencies.
+* Added wrapper functions around basic statistical tests to compare cell population frequencies between groups of samples (`frequency_t_test()`, `frequency_wilcox_test()`, `frequency_anova_test()`, `frequency_kruskal_test()`, `frequency_friedman_test()`) 
+* Added `prepInputDiffcyt()` function to transform the `condor` object into an SummarizedExperiment object compatible with the `diffcyt` package for differential testing.
+* Renaming of arguments in `runPseudotime()` function to harmonize within the package
+* Renaming of arguments in `metaclustering()` function to harmonize within the package
+* Updated documentation
+* Renaming of arguments in multiple function to harmonize within the package
+* Setting a default seed in multiple functions
+* Added functions to use the `CytoNorm` algorithm for batch normalization
+* Bug fixes in `prep_flw()` when merging annotation and removing parameters, saving of import parameters in extras slot of fcd
+* Added new parameters in `runFlowSOM()` to determine size of FlowSOM grid
+* implemented marker selection (`runPCA()`, `runUMAP()`, `runDM()`, `runtSNE()`, `runPhenograph()`, `runFlowSOM()`), saving of marker selection in extra slot of fcd
+* Added functions to extract all markers present in fcd (`measured_markers()`) or selected markers (`used_markers()`)
+* Added function to visualize PC loadings
+* Simplified data loading and transformation function including useful error messages
+* Included `arcsinh` transformation with cofactor 5 for cyTOF data
+
 # cyCONDOR 0.1.5
 
 * Fix bug in the definition of tab separator when loading csv files

NEWS.md

@@ -1,14 +1,17 @@
-#' runAstir_celltype
+#' Run Astir cell type prediction
 #'
-#' @title runAstir_celltype
-#' @description Predict cell types using Astir. This package requires the python library `astir` and `reticulate` to work.
+#' @title Run Astir cell type prediction
+#' @description Predict cell types using 'Astir'. This package requires the python library `astir` and `reticulate` to work.
+#' The function returns a `condor` object with automatically annotated cell types and QC of the annotation, the results are also saved in a folder specified by the user.
 #' @param fcd Flow cytometry dataset.
 #' @param data_slot Data slot to use for the analysis (e.g. "orig" or "norm").
 #' @param analysis_path Full path to the output folder of astir analysis.
 #' @param manifest_name Filename of the manifest file, this file must be located in the `analysis_path` folder.
-#' @param max_epochs Maximum number of epochs.
+#' @param max_epochs Maximum number of epochs, for details see `Astir` documentation.
 #' @param learning_rate Learning Rate.
-#' @param initial_epochs Initial Epochs.
+#' @param initial_epochs initial epochs, for details see `Astir` documentation.
+#' @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
 #' @return runAstir_celltype
 #'
@@ -70,10 +73,11 @@ runAstir_celltype <- function(fcd,
 
 }
 
-#' runAstir_cellstates
+#' Run Astir cell state prediction
 #'
 #' @title runAstir_cellstates
 #' @description Predict cell states using Astir. This package requires the python library `astir` and `reticulate` to work.
+#' The function returns a `condor` object with automatically annotated cell states and QC of the annotation, the results are also saved in a folder specified by the user.
 #' @param fcd Flow cytometry dataset.
 #' @param data_slot Data slot to use for the analysis (e.g. "orig" or "norm").
 #' @param analysis_path Full path to the output folder of astir analysis.