Created corr analysis function

.Rhistory

@@ -1,27 +1,3 @@
-n_per_group = 10,
-cells_per_case = 20,
-cells_per_control = 20,
-ncells_variation_type = "Poisson",
-pval = 0.05,
-foldchange = 2)
-error_hierarchicell(data_summ,
-method = "Pseudobulk_mean",
-n_genes = 1000,
-n_per_group = 10,
-cells_per_case = 3,
-cells_per_control = 3,
-ncells_variation_type = "Poisson",
-pval = 0.05,
-foldchange = 2)
-error_hierarchicell(data_summ,
-method = "Pseudobulk_mean",
-n_genes = 1000,
-n_per_group = 10,
-cells_per_case = 300,
-cells_per_control = 300,
-ncells_variation_type = "Poisson",
-pval = 0.05,
-foldchange = 2)
 error_hierarchicell(data_summ,
 method = "Pseudobulk_mean",
 n_genes = 1000,
@@ -473,40 +449,64 @@ library(Hmisc)
 ?select
 ?select
 ?setnames
-?quantile
-?as.formula
-library(rworkflows)
-getwd()
-setwd("../Power_Analysis_package/")
-rworkflows::use_workflow()
-getwd()
-rworkflows::use_workflow()
-rworkflows::use_workflow()
-rworkflows::use_workflow(branches=c("master","main","devel","RELEASE_**","Rworkflows_test"),save_dir="C:/Users/salma/Power_Analysis_package")
-rworkflows::use_workflow(branches=c("master","main","devel","RELEASE_**","Rworkflows_test"),save_dir="C:/Users/salma/Power_Analysis_package/.github")
-here::here
-here::here(".git","w")
-rworkflows::use_workflow(branches=c("master","main","devel","RELEASE_**","Rworkflows_test"),save_dir="C:/Users/salma/Power_Analysis_package/.github/workflows")
-getwd()
-devtools::check()
-getwd()
-devtools::load_all()
+?rowSums
+Matrix::rowSums
+?Matrix::rowSums
+?select
+library(Hmisc)
+?select
+?get
+?names
+?aes
+?factor
+?unique
+library(ensembldb)
+browseVignettes("ensembldb")
+?lapply
+?element_text
+?duplicted
+?duplicated
+?length
+?sapply
+?as.character
+?matrix
+?unique
+conflicts()
+conflicts()
+library(BiocGenerics)
+conflicts()
+?geom_bar_repel
+library(ggrepel)
+?geom_bar_repel
+library(ggplot2)
+geom_bar_repel
+?geom_bar_repel
+?get
+?select
+?scales
+?percent
+?unit
+library(ggplot2)
+?unit
+class("hello")
+test <- list(1,2,3)
+test
+for(j in list){
+for(j in list){
+print(j)
+}
+for(j in test){
+print(j)
+}
+test <- c(1,2,3)
+for(j in test){
+print(j)
+}
 getwd()
+setwd("C:/Users/salma/Power_Analysis_package")
 devtools::document()
-?usethis::use_vignette()
-usethis::use_vignette("poweranalysis")
+#usethis::use_vignette("poweranalysis")
 devtools::load_all()
-sessionInfo()
-getwd()
-devtools::document()
-devtools::document()
-warnings()
-devtools::document()
-?geom_bar_repel
-devtools::document()
-install.packages("roxygen2")
-install.packages("roxygen2")
-install.packages("roxygen2")
-install.packages("roxygen2")
-library(roxygen2)
-packageVersion("roxygen2")
+devtools::install()
+devtools::check()
+devtools::build()

R/correlation_analysis.r

@@ -23,8 +23,20 @@ correlation_analysis <- function(dataset_name="placeholder",
                                  numSubsets="placeholder",
                                  output_path=getwd()){
 
-    # create correlation plots for each p-value cut-off
-
-    return("TestOut")
+    # run plot_mean_correlation for each p-value (saving outputs)
+    mean_correlation_results <- plot_mean_correlation(dataset_name,
+                                                      allstudies,
+                                                      celltypes,
+                                                      pvals,
+                                                      data_names,
+                                                      output_path)
+
+    # run correlation_boxplots for each p-value (saving outputs)
+    boxplot_results <- correlation_boxplots(mean_correlation_results,
+                                            numRealDatasets=length(allstudies),
+                                            pvals=pvals,
+                                            output_path=output_path)
+
+    return(list(mean_correlation_results = mean_correlation_results, boxplot_results = boxplot_results))
 
 }