From fd10e742addfe73c92861bccd9dd0b6394efec9b Mon Sep 17 00:00:00 2001
From: Jacob Wagner <jpwagner@fredhutch.org>
Date: Wed, 11 Dec 2019 10:56:50 -0800
Subject: [PATCH] Allow negative subsetting of columns in cytoframe/cytoset

---
 R/cytoframe.R                 | 11 +++++++++--
 R/cytoset.R                   |  8 ++++++++
 tests/testthat/test-cytoset.R |  5 +++++
 3 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/R/cytoframe.R b/R/cytoframe.R
index 7d422a52..34431a35 100644
--- a/R/cytoframe.R
+++ b/R/cytoframe.R
@@ -427,8 +427,15 @@ setMethod("[",
             stop(msg, call.=FALSE)
         }
             
-        if(is.numeric(j)||is.integer(j))    
-          subset_cytoframe_by_cols(fr@pointer, j - 1)
+        if(is.numeric(j)||is.integer(j)){
+        	if(any(j < 0)){
+        		if(!all(j <= 0)){
+        			stop("Cannot mix positive and negative subscripts")
+        		}
+        		j <- (1:length(colnames(x)))[j]
+        	}
+        	subset_cytoframe_by_cols(fr@pointer, j - 1)
+        }    
         else
           stop("invalid j index!")
       }
diff --git a/R/cytoset.R b/R/cytoset.R
index 57dbd5e5..2e6cc7ba 100644
--- a/R/cytoset.R
+++ b/R/cytoset.R
@@ -685,6 +685,14 @@ setMethod("[",
 			
 	    if(missing(j))
 	      j <- NULL
+	    if(is.numeric(j)||is.integer(j)){
+	    	if(any(j < 0)){
+	    		if(!all(j <= 0)){
+	    			stop("Cannot mix positive and negative subscripts")
+	    		}
+	    		j <- (1:length(colnames(x)))[j]
+	    	}
+	    }
 	    x <- copy_view(x)
 	    subset_cytoset(x@pointer, i, j)
 	    x
diff --git a/tests/testthat/test-cytoset.R b/tests/testthat/test-cytoset.R
index 31bf56f0..c51de9aa 100644
--- a/tests/testthat/test-cytoset.R
+++ b/tests/testthat/test-cytoset.R
@@ -86,6 +86,11 @@ test_that("[", {
       expect_equal(sampleNames(cs1[-c(3,7,11)]), sampleNames(cs1)[-c(3,7,11)])
       expect_error(cs1[c(-3, 7, -11)], "Cannot mix positive and negative subscripts")
       
+      #Test negative subsetting of columns for cytoset and cytoframe
+      expect_equal(colnames(cs1[,-c(3,5)]), colnames(cs1)[-c(3,5)])
+      cf1 <- cs1[[1]]
+      expect_equal(colnames(cf1[,-c(2,4)]), colnames(cf1)[-c(2,4)])
+      
     })
 
 test_that("subset", {