use SummarizedExperiment instead of loose data structures

NAMESPACE

@@ -32,8 +32,10 @@ export(metaproviz_config_path)
 export(metaproviz_load_config)
 export(metaproviz_reset_config)
 export(metaproviz_save_config)
+import(ggfortify)
 importFrom(KEGGREST,keggGet)
 importFrom(KEGGREST,keggList)
+importFrom(MatrixGenerics,rowMins)
 importFrom(OmnipathR,ambiguity)
 importFrom(OmnipathR,config_path)
 importFrom(OmnipathR,id_types)
@@ -45,6 +47,7 @@ importFrom(OmnipathR,reset_config)
 importFrom(OmnipathR,save_config)
 importFrom(OmnipathR,set_loglevel)
 importFrom(OmnipathR,translate_ids)
+importFrom(S4Vectors,DataFrame)
 importFrom(broom,tidy)
 importFrom(dplyr,across)
 importFrom(dplyr,arrange)
@@ -101,6 +104,7 @@ importFrom(ggplot2,scale_shape_manual)
 importFrom(ggplot2,scale_x_continuous)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,stat_summary)
+importFrom(ggplot2,sym)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
@@ -157,6 +161,7 @@ importFrom(stats,bartlett.test)
 importFrom(stats,kruskal.test)
 importFrom(stats,lm)
 importFrom(stats,p.adjust)
+importFrom(stats,p.adjust.methods)
 importFrom(stats,shapiro.test)
 importFrom(stringr,str_match)
 importFrom(stringr,str_remove)
@@ -169,6 +174,7 @@ importFrom(tibble,rownames_to_column)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,separate)
+importFrom(tidyr,separate_longer_delim)
 importFrom(tidyr,separate_rows)
 importFrom(tidyr,unite)
 importFrom(tidyselect,all_of)

R/HelperLog.R

@@ -34,8 +34,8 @@
 #'
 #' @seealso \code{\link{metaproviz_log}}
 MetaProViz_logfile <- function(){
-  #Creates the path for the log file
-  OmnipathR::logfile('MetaProViz')
+    ## Creates the path for the log file
+    OmnipathR::logfile('MetaProViz')
 }
 
 
@@ -56,8 +56,8 @@ MetaProViz_logfile <- function(){
 #' @seealso \code{\link{metaproviz_logfile}}
 #'
 MetaProViz_log <- function(){
-  #Opens log file for browsing
-  OmnipathR::read_log('MetaProViz')
+    ## opens log file for browsing
+    OmnipathR::read_log('MetaProViz')
 }
 
 
@@ -82,34 +82,36 @@ MetaProViz_set_loglevel <- function(level, target = 'logfile'){
 #'
 #' @noRd
 MPV_trace <- function() {#MPV=MetaProViz
-  # Useful for debugging
-  MetaProViz_set_loglevel('trace', target = 'console')
+    ## Useful for debugging
+    MetaProViz_set_loglevel("trace", target = "console")
 }
 
 #' Set the console log level to "trace"
 #'
-#' @importFrom OmnipathR set_loglevel
+#' @importFrom OmnipathR set_loglevel 
 #' @importFrom logger log_info
 #' @importFrom utils packageVersion
 #'
 #' @noRd
 #'
 MetaProViz_Init <- function(){
-  # Only run the first time a MetaProViz function is used in an environment --> Creates log file
-  if(is.null(metaproviz.env$init)){
-    #Initial log
-    OmnipathR:::init_config(pkg = "MetaProViz")
-    OmnipathR:::init_log(pkg = "MetaProViz")
-    log_info('Welcome to MetaProViz!')
-    log_info('MetaProViz version: %s', packageVersion("MetaProViz"))
+
+    ## only run the first time a MetaProViz function is used in an 
+    ## environment --> Creates log file
+    if (is.null(metaproviz.env$init)) {
+        ## initial log
+        OmnipathR:::init_config(pkg = "MetaProViz")
+        OmnipathR:::init_log(pkg = "MetaProViz")
+        log_info("Welcome to MetaProViz!")
+        log_info("MetaProViz version: %s", packageVersion("MetaProViz"))
 
-    #Do we run in a build server like bioconductor?
-    buildserver <- OmnipathR:::.on_buildserver()
+        ## Do we run in a build server like bioconductor?
+        buildserver <- OmnipathR:::.on_buildserver()
 
-    if(buildserver){
-      set_loglevel('trace', target = 'console', pkg = "MetaProViz")
-    }
+        if (buildserver) {
+            set_loglevel("trace", target = "console", pkg = "MetaProViz")
+        }
 
-    metaproviz.env$init <- TRUE
-  }
+        metaproviz.env$init <- TRUE
+    }
 }

R/HelperOptions.R

@@ -1,7 +1,7 @@
 
 .metaproviz_options_defaults <- list(
-  metaproviz.loglevel = 'trace',
-  metaproviz.console_loglevel = 'success'
+   metaproviz.loglevel = "trace",
+    metaproviz.console_loglevel = "success"
 )
 
 
@@ -28,13 +28,11 @@
 #' @importFrom OmnipathR save_config
 #' @export
 metaproviz_save_config <- function(
-        path = NULL,
-        title = 'default',
-        local = FALSE
-    ){
-
-    save_config(path = path, title = title, local = local, pkg = 'MetaProViz')
+    path = NULL,
+    title = "default",
+    local = FALSE) {
 
+    save_config(path = path, title = title, local = local, pkg = "MetaProViz")
 }
 
 
@@ -61,20 +59,18 @@ metaproviz_save_config <- function(
 #' @importFrom OmnipathR load_config
 #' @export
 metaproviz_load_config <- function(
-        path = NULL,
-        title = 'default',
-        user = FALSE,
-        ...
-    ){
+    path = NULL,
+    title = "default",
+    user = FALSE,
+    ...) {
 
     load_config(
         path = path,
         title = title,
         user = user,
-        pkg = 'MetaProViz',
+        pkg = "MetaProViz",
         ...
     )
-
 }
 
 
@@ -100,7 +96,7 @@ metaproviz_load_config <- function(
 #' @seealso \code{\link{metaproviz_load_config}, \link{metaproviz_save_config}}
 metaproviz_reset_config <- function(save = NULL, reset_all = FALSE) {
 
-   reset_config(save = save, reset_all = reset_all, pkg = 'MetaProViz')
+   reset_config(save = save, reset_all = reset_all, pkg = "MetaProViz")
 
 }
 
@@ -117,8 +113,8 @@ metaproviz_reset_config <- function(save = NULL, reset_all = FALSE) {
 #'
 #' @importFrom OmnipathR config_path
 #' @export
-metaproviz_config_path <- function(user = FALSE){
+metaproviz_config_path <- function(user = FALSE) {
 
-    config_path(user = user, pkg = 'MetaProViz')
+    config_path(user = user, pkg = "MetaProViz")
 
 }