Updated website for version 0.3.0

Author: lorenzobonaguro

DESCRIPTION

@@ -13,7 +13,7 @@ Authors@R: c(
   )
 Description: Flow cytometry analysis workflow. The aim of this project is to 
     provide an intuitive workflow for the analysis of high-dimensionality cytometry data in R.
-URL: https://github.com/lorenzobonaguro/cyCONDOR
+URL: https://lorenzobonaguro.github.io/cyCONDOR
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 biocViews:

NEWS.md

@@ -9,9 +9,9 @@
 * Developed a function (`condor_session_info`) to include the `SessionInfo` to the `condor` object to increase tackability of the analysis.
 * Included storage of the statistical test results in the `condor` object
 * Added the option to display statistics to the `plot_frequency_boxplot` function - so far for `wilcox`, `t_test` and `diffcyt`
-* Added a function to write FCS files from a `condor` object (`write_fcs`)
 * Added function to correlate the cyCONDOR results and the manual gating with FlowJo or similar software (`corr_plot_comparison`)
 * Companion Docker image is not multi-platform `amd64` and `arm64` for better performance on Mac
+* **Experimental**: Added a function to write FCS files from a `condor` object (`write_fcs`). Currently the function if writing in the .fcs file the cyCONDOR transformed values, we will change to the original values in the next iteration after more extensive testing.
 
 # cyCONDOR 0.2.1
 * Included help function to assign metaclusters (Thanks to Lucas Secchim Ribeiro)

R/data_load_and_transform.R

@@ -551,6 +551,10 @@ write_fcs <- function(fcd = condor,
                       dir = paste0(getwd(), "/"),
                       filename){
 
+  # Print a working to let people know this is an experimental functio
+  warning("This function is still experimental. Feel free to test if and report your experience, this function
+  is currently writing cyCONDOR transformed value, future revision will export original values.")
+
   # Get the expression data
   xdata <- fcd[["expr"]][[expr_slot]]
   exp <- xdata

_pkgdown.yml

@@ -83,6 +83,7 @@ reference:
   - frequency_wilcox_test
   - prepInputDiffcyt
   - marker_wilcox_test
+  - add_diffcyt_statistics
 
 - title: Utilities
   desc:  Collection of misc functions.
@@ -96,9 +97,13 @@ reference:
   - merge_condor
   - subset_fcd
   - subset_fcd_byparam
+  - subsample_geosketch
   - checkInput
   - measured_markers
   - create_metaclustering_script
+  - condor_session_info
+  - corr_plot_comparison
+  - write_fcs
 
 articles:
 - title: Detailed cyCONDOR workflows