add group counts to output of summary functions

Author: clabornd

R/summarizeGroupComparisons.R

@@ -94,7 +94,8 @@ getGroupComparisonSummaryFunctionNames <- function() {
   })
 
   new_fdata <- do.call(rbind, lapply(edata_cols, function(x) attr(x, "f_data")))
-  new_edata <- data.frame(compData$e_data[, getEDataColName(compData)], do.call(cbind, edata_cols))
+  new_fdata$Comparison_Summary_Column <- make.unique(new_fdata$Comparison_Summary_Column)
+  new_edata <- data.frame(setNames(compData$e_data[, getEDataColName(compData)], getEDataColName(compData)), do.call(cbind, edata_cols))
   colnames(new_edata)[1] <- getEDataColName(compData)
 
   if (inherits(compData, "peakData")) {

R/uniqueness_functions.R

@@ -81,7 +81,13 @@ uniqueness_nsamps <- function(edata_df, group_df, data_scale, pres_thresh, absn_
   res_vec[which(numpres$N_grp1 <= absn_thresh & numpres$N_grp2 >= pres_thresh)] = paste("Unique to", grps[2], sep = " ")
 
   lvls <- c(paste("Unique to", grps), "Observed in Both")
-  data.frame(uniqueness_nsamps = factor(res_vec, levels = lvls))
+  out_df = data.frame(uniqueness_nsamps = factor(res_vec, levels = lvls))
+  out_df = dplyr::bind_cols(
+    out_df,
+    numpres
+  )
+  
+  return(out_df)
 }
 
 
@@ -161,7 +167,16 @@ uniqueness_prop <- function(edata_df, group_df, data_scale, pres_thresh, absn_th
   res_vec[which(prop_pres$prop_grp1 <= absn_thresh & prop_pres$prop_grp2 >= pres_thresh)] = paste("Unique to", grps[2], sep = " ")
 
   lvls <- c(paste("Unique to", grps), "Observed in Both")
-  data.frame(uniqueness_prop = factor(res_vec, levels=lvls))
+  out_df = data.frame(
+    uniqueness_prop = factor(res_vec, levels=lvls)
+  )
+  
+  out_df = dplyr::bind_cols(
+    out_df,
+    prop_pres
+  )
+  
+  return(out_df)
 }
 
 

tests/testthat/test_summarizeComparisons.R

@@ -70,13 +70,13 @@ test_that("test of summarizeGroupComparisons with multiple summary functions on
 
   expect_true(inherits(grpCompSummary, "comparisonSummary"))
   expect_false(inherits(grpCompSummary, "groupComparison"))
-  expect_equal(ncol(grpCompSummary$e_data), 7)
+  expect_equal(ncol(grpCompSummary$e_data), 11)
   expect_true(getEDataColName(grpComp) %in% colnames(grpCompSummary$e_data))
   expect_true(all(dim(grpComp$e_meta) == dim(grpCompSummary$e_meta)))
   expect_true(all(colnames(grpComp$e_meta) %in% colnames(grpCompSummary$e_meta)))
   expect_true(all(c("uniqueness_gtest", "uniqueness_nsamps", "uniqueness_prop") %in% 
                     grpCompSummary$f_data$Summary_Function_Name))
-  expect_equal(nrow(grpCompSummary$f_data), 6)
+  expect_equal(nrow(grpCompSummary$f_data), 10)
   expect_true(all(unlist(lapply(grpCompSummary$e_data[, 2], function(x) is.factor(x)))))
 
 })