update run_phenomix to run multiple CTD levels

.gitignore

@@ -15,3 +15,53 @@ tests/testthat/data/
 ./**/**/**/**/.DS_Store
 ./**/**/**/**/**/.DS_Store
 ./**/**/**/**/**/**/.DS_Store
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MSTExplorer
 Title: Multi-Scale Target Explorer
-Version: 1.0.3
+Version: 1.0.4
 Authors@R:
     c(
     person(given = "Brian",
@@ -25,7 +25,7 @@ Encoding: UTF-8
 URL: https://github.com/neurogenomics/MSTExplorer
 BugReports: https://github.com/neurogenomics/MSTExplorer/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.1)
 Imports:

NEWS.md

@@ -1,3 +1,9 @@
+# MSTExplorer 1.0.4
+
+## New features
+
+* `run_phenomix`: can now take multiple `annotLevel`s at once (will iterate).
+
 # MSTExplorer 1.0.3
 
 ## New features

R/run_phenomix.R

@@ -19,14 +19,13 @@
 #'                          save_path=tempfile())
 #' }
 run_phenomix <- function(ctd_name,
-                         annotLevel,
+                         annotLevel = seq(length(ctd)),
                          ymat,
                          test_method="glm",
                          metric="specificity",
                          ctd = load_example_ctd(
                            file = paste0("ctd_",ctd_name,".rds")
                            ),
-                         xmat = ctd[[annotLevel]][[metric]],
                          save_path = file.path(
                            tempfile(),
                            # here::here(),
@@ -49,18 +48,22 @@ run_phenomix <- function(ctd_name,
     test_method <- "glm"
     multivariate <- FALSE
   }
-  lm_res <- phenomix::iterate_lm(xmat = xmat,
-                                 ymat = ymat,
-                                 test_method = test_method,
-                                 multivariate = multivariate,
-                                 workers = workers,
-                                 ...)
+  ## Iterate over each CTD level
+  lm_res <- lapply(stats::setNames(annotLevel,annotLevel), function(lvl){
+    messager("Running phenomix with CTD annotLevel:",lvl)
+    phenomix::iterate_lm(xmat = ctd[[lvl]][[metric]],
+                         ymat = ymat,
+                         test_method = test_method,
+                         multivariate = multivariate,
+                         workers = workers,
+                         ...)
+  }) |> data.table::rbindlist(idcol = "annotLevel")
+
   run_phenomix_postprocess <- function(lm_res,
                                        annotLevel,
                                        effect_var = c("estimate","statistic",
                                                       "ges","F")){
     effect_var <- intersect(effect_var,names(lm_res))[1]
-    lm_res[,annotLevel:=annotLevel]
     data.table::setnames(lm_res,
                          c("xvar","yvar"),
                          c("CellType","hpo_id"))