From ab056fc6b0e09dba30c3f57f47b654e493e1e90f Mon Sep 17 00:00:00 2001
From: Antoine Sachet <antoine.sac@gmail.com>
Date: Wed, 28 Oct 2020 18:35:01 +0000
Subject: [PATCH 1/7] Make network_plot work with 2 variables. Close #118

---
 R/cor_df.R                  |  9 +++++++--
 tests/testthat/test-plots.R | 12 ++++++++++--
 2 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/R/cor_df.R b/R/cor_df.R
index 0d17de4..4d15cd4 100644
--- a/R/cor_df.R
+++ b/R/cor_df.R
@@ -192,8 +192,13 @@ network_plot.cor_df <- function(rdf,
   rdf <-  as_matrix(rdf, diagonal = 1)
   distance <- 1 - abs(rdf)
 
-  # Use multidimensional Scaling to obtain x and y coordinates for points.
-  points <- suppressWarnings(stats::cmdscale(distance))
+  points <- if (ncol(rdf) == 2) {
+    # 2 vars: 2 opposing points
+    matrix(c(0, -0.1, 0, 0.1), ncol = 2, dimnames = list(colnames(rdf)))
+  } else {
+    # More than 2 vars: multidimensional scaling to obtain x and y coordinates for points.
+    suppressWarnings(stats::cmdscale(distance, k = 2))
+  }
 
   if(ncol(points) < 2){
 
diff --git a/tests/testthat/test-plots.R b/tests/testthat/test-plots.R
index 12265ae..9fc8b30 100644
--- a/tests/testthat/test-plots.R
+++ b/tests/testthat/test-plots.R
@@ -2,16 +2,24 @@ d <- datasets::anscombe[, 1:7]
 d[1, 1] <- NA
 d <- correlate(d)
 
-context("network")
+context("network_plot")
 
 test_that("Network plot works", {
   expect_s3_class(network_plot(d), "ggplot")
   expect_s3_class(network_plot(d, colors = c("indianred2", "white", "skyblue1")), "ggplot")
 })
 
+
+test_that("Network plot works with 2 variables", {
+  d2 <- correlate(datasets::anscombe[c("x1", "y1")])
+
+  expect_s3_class(network_plot(d2), "ggplot")
+  expect_s3_class(network_plot(d2, colors = c("indianred2", "white", "skyblue1")), "ggplot")
+})
+
 context("rplot")
 
-test_that("Network plot works", {
+test_that("rplot works", {
   expect_s3_class(rplot(d), "ggplot")
   expect_s3_class(rplot(d, colors = c("indianred2", "white", "skyblue1")), "ggplot")
 })

From 170e5717ec0119de152608936aa4f86d97252229 Mon Sep 17 00:00:00 2001
From: Antoine Sachet <antoine.sac@gmail.com>
Date: Wed, 28 Oct 2020 18:43:14 +0000
Subject: [PATCH 2/7] Fix subsetting that failed on single column df. Close
 #119

---
 R/cor_df.R                     | 6 +++---
 R/reshape.R                    | 2 +-
 R/utility.R                    | 2 +-
 tests/testthat/test-as_cordf.R | 6 ++++++
 4 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/R/cor_df.R b/R/cor_df.R
index 4d15cd4..637c94c 100644
--- a/R/cor_df.R
+++ b/R/cor_df.R
@@ -5,7 +5,7 @@ as_matrix.cor_df <- function(x, diagonal) {
 
   # Separate rownames
   row_name <- x$rowname
-  x <- x[, colnames(x) != "rowname"]
+  x <- x[colnames(x) != "rowname"]
   # Convert to matrix and set rownames
   class(x) <- "data.frame"
   x <- as.matrix(x)
@@ -22,7 +22,7 @@ shave.cor_df <- function(x, upper = TRUE) {
 
   # Separate rownames
   row_name <- x$rowname
-  x <- x[, colnames(x) != "rowname"]
+  x <- x[colnames(x) != "rowname"]
 
   # Remove upper matrix
   if (upper) {
@@ -93,7 +93,7 @@ focus_if.cor_df <- function(x, .predicate, ..., mirror = FALSE) {
 
   # Identify which variables to keep
   to_keep <- map_lgl(
-    x[, colnames(x) != "rowname"],
+    x[colnames(x) != "rowname"],
     .predicate, ...
   )
 
diff --git a/R/reshape.R b/R/reshape.R
index e50f3c9..5577c26 100644
--- a/R/reshape.R
+++ b/R/reshape.R
@@ -124,7 +124,7 @@ stretch <- function(x, na.rm = FALSE, remove.dups =  FALSE) {
 stretch.cor_df <- function(x, na.rm = FALSE, remove.dups =  FALSE) {
   if(remove.dups) x <- shave(x)
   row_name <- x$rowname
-  x <- x[, colnames(x) != "rowname"]
+  x <- x[colnames(x) != "rowname"]
   tb <- imap_dfr(x, ~tibble(x = .y, y = row_name, r = .x))
   if(na.rm) tb <- tb[!is.na(tb$r), ]
   if(remove.dups) {
diff --git a/R/utility.R b/R/utility.R
index efef515..d85cff9 100644
--- a/R/utility.R
+++ b/R/utility.R
@@ -20,7 +20,7 @@ as_cordf <- function(x, diagonal = NA) {
   }
   x <- as.data.frame(x)
   row_name <- x$rowname
-  x <- x[, colnames(x) != "rowname"]
+  x <- x[colnames(x) != "rowname"]
   rownames(x) <- row_name
   if(ncol(x) != nrow(x)) {
     stop("Input object x is not a square. ",
diff --git a/tests/testthat/test-as_cordf.R b/tests/testthat/test-as_cordf.R
index 3e4e0ca..34aab94 100644
--- a/tests/testthat/test-as_cordf.R
+++ b/tests/testthat/test-as_cordf.R
@@ -18,3 +18,9 @@ test_that("Diagonal sets correctly", {
   expect_equal(all(is.na(diag(as.matrix(as_cordf(d, diagonal = NA)[, -1])))), TRUE)
   expect_equal(all(diag(as.matrix(as_cordf(d, diagonal = 100)[, -1] == 100))), TRUE)
 })
+
+test_that("as_cordf handles single correlation", {
+  d1 <- cor(mtcars["cyl"])
+  expect_s3_class(as_cordf(d1), "cor_df")
+  expect_equal(colnames(as_cordf(d1)), c("rowname", colnames(d1)))
+})

From ce1f5c112e67be2d832294216edd336aedc07528 Mon Sep 17 00:00:00 2001
From: Antoine Sachet <antoine.sac@gmail.com>
Date: Wed, 28 Oct 2020 19:25:28 +0000
Subject: [PATCH 3/7] correlate() no longer sets the diagonal of 1x1
 correlation matrix.

As a side effect, correlate() now works with numeric vectors and one-column dfs.

Close #120. Close #121.
---
 R/utility.R                     |  2 +-
 tests/testthat/test-correlate.R | 13 +++++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/R/utility.R b/R/utility.R
index d85cff9..e09d70c 100644
--- a/R/utility.R
+++ b/R/utility.R
@@ -26,7 +26,7 @@ as_cordf <- function(x, diagonal = NA) {
     stop("Input object x is not a square. ",
          "The number of columns must be equal to the number of rows.")
   }
-  diag(x) <- diagonal
+  if (ncol(x) > 1) diag(x) <- diagonal
   new_cordf(x, names(x))
 }
 
diff --git a/tests/testthat/test-correlate.R b/tests/testthat/test-correlate.R
index ea970f1..5062d56 100644
--- a/tests/testthat/test-correlate.R
+++ b/tests/testthat/test-correlate.R
@@ -18,3 +18,16 @@ test_that("Diagonal sets correctly", {
   expect_equal(all(is.na(diag(as.matrix(correlate(d, diagonal = NA)[, -1])))), TRUE)
   expect_equal(all(diag(as.matrix(correlate(d, diagonal = 100)[, -1] == 100))), TRUE)
 })
+
+
+test_that("correlate works with numeric vectors", {
+  expect_equal(correlate(x = 1:10, y = 1:10)[[2]], 1)
+  expect_equal(correlate(x = 1:10, y = -(1:10), diagonal = 0)[[2]], -1)
+})
+
+test_that("correlate works with a one-column data.frame", {
+  var <- "Sepal.Length"
+  expect_equal(correlate(datasets::iris[var])[[1]], var)
+  expect_equal(correlate(datasets::iris[var])[[2]], 1)
+
+})

From dabde2b7ed98ef9fb652daee2128871c18b54bff Mon Sep 17 00:00:00 2001
From: Antoine Sachet <antoine.sac@gmail.com>
Date: Wed, 28 Oct 2020 19:30:40 +0000
Subject: [PATCH 4/7] network_plot() now works with a single variable. Close
 #118 again :)

---
 R/cor_df.R                  | 5 ++++-
 tests/testthat/test-plots.R | 6 ++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/R/cor_df.R b/R/cor_df.R
index 637c94c..7f26bbc 100644
--- a/R/cor_df.R
+++ b/R/cor_df.R
@@ -192,7 +192,10 @@ network_plot.cor_df <- function(rdf,
   rdf <-  as_matrix(rdf, diagonal = 1)
   distance <- 1 - abs(rdf)
 
-  points <- if (ncol(rdf) == 2) {
+  points <- if (ncol(rdf) == 1) {
+    # 1 var: a single central point
+    matrix(c(0, 0), ncol = 2, dimnames = list(colnames(rdf)))
+  } else if (ncol(rdf) == 2) {
     # 2 vars: 2 opposing points
     matrix(c(0, -0.1, 0, 0.1), ncol = 2, dimnames = list(colnames(rdf)))
   } else {
diff --git a/tests/testthat/test-plots.R b/tests/testthat/test-plots.R
index 9fc8b30..4bb34f5 100644
--- a/tests/testthat/test-plots.R
+++ b/tests/testthat/test-plots.R
@@ -17,6 +17,12 @@ test_that("Network plot works with 2 variables", {
   expect_s3_class(network_plot(d2, colors = c("indianred2", "white", "skyblue1")), "ggplot")
 })
 
+test_that("Network plot works with 1 variable", {
+  d1 <- correlate(datasets::anscombe["x1"])
+  expect_s3_class(network_plot(d1), "ggplot")
+  expect_s3_class(network_plot(d1, colors = c("indianred2", "white", "skyblue1")), "ggplot")
+})
+
 context("rplot")
 
 test_that("rplot works", {

From 0a4b33034f15af14c486979dfdf4dd3cd52ba19d Mon Sep 17 00:00:00 2001
From: Antoine Sachet <antoine.sac@gmail.com>
Date: Wed, 28 Oct 2020 19:38:10 +0000
Subject: [PATCH 5/7] Update NEWS and contributors

---
 DESCRIPTION          | 4 +++-
 NEWS.md              | 5 +++++
 man/corrr-package.Rd | 5 +++++
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index d28923d..65727d4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,9 @@ Authors@R:
             role = c("aut")),
       person(given = "Jorge",
             family = "Cimentada",
-            role = c("aut"))                      
+            role = c("aut")),
+      person(given = "Sachet", family = "Antoine",
+             email = "antoine.sac@gmail.com", role = "ctb")                         
              )
 Depends: 
     R (>= 3.3.0)
diff --git a/NEWS.md b/NEWS.md
index a3b0a2b..26446d5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,6 +8,11 @@
 
 - Make `network_plot()` more robust, for example to highly correlated data (@thisisdaryn, #107)
 
+- `correlate()` now works with single-column data.frames and numeric vectors (@antoine-sachet, #122)
+
+- `network_plot()` now works with `cor_df` objects with only 1 or 2 columns (@antoine-sachet, #122)
+
+
 # corrr 0.4.2
 
 - Updates to work with tibble 3.0.0  and dplyr 1.0.0
diff --git a/man/corrr-package.Rd b/man/corrr-package.Rd
index bfd5a5a..26204c3 100644
--- a/man/corrr-package.Rd
+++ b/man/corrr-package.Rd
@@ -33,5 +33,10 @@ Authors:
   \item Jorge Cimentada
 }
 
+Other contributors:
+\itemize{
+  \item Sachet Antoine \email{antoine.sac@gmail.com} [contributor]
+}
+
 }
 \keyword{internal}

From 1341e0ffc935c05b8f8800c699efda22ed962081 Mon Sep 17 00:00:00 2001
From: Antoine Sachet <antoine.sac@gmail.com>
Date: Wed, 28 Oct 2020 20:17:19 +0000
Subject: [PATCH 6/7] Make it clear in the NEWS that the diagonal is not set
 for 1x1 correlation matrices.

---
 NEWS.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 26446d5..2422c70 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -9,7 +9,8 @@
 - Make `network_plot()` more robust, for example to highly correlated data (@thisisdaryn, #107)
 
 - `correlate()` now works with single-column data.frames and numeric vectors (@antoine-sachet, #122)
-
+  Note the `diagonal` argument is ignored in these 2 cases.
+  
 - `network_plot()` now works with `cor_df` objects with only 1 or 2 columns (@antoine-sachet, #122)
 
 

From 11a55640204aa1d4312da0b88a5c7d91d0a1b922 Mon Sep 17 00:00:00 2001
From: Antoine Sachet <antoine.sac@gmail.com>
Date: Sun, 1 Nov 2020 19:40:08 +0000
Subject: [PATCH 7/7] Address PR feedback

---
 DESCRIPTION          | 5 +----
 NEWS.md              | 3 +--
 man/corrr-package.Rd | 5 -----
 3 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 65727d4..260988f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,10 +18,7 @@ Authors@R:
             role = c("aut")),
       person(given = "Jorge",
             family = "Cimentada",
-            role = c("aut")),
-      person(given = "Sachet", family = "Antoine",
-             email = "antoine.sac@gmail.com", role = "ctb")                         
-             )
+            role = c("aut")))
 Depends: 
     R (>= 3.3.0)
 Imports: 
diff --git a/NEWS.md b/NEWS.md
index 2422c70..a6a1c60 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -8,8 +8,7 @@
 
 - Make `network_plot()` more robust, for example to highly correlated data (@thisisdaryn, #107)
 
-- `correlate()` now works with single-column data.frames and numeric vectors (@antoine-sachet, #122)
-  Note the `diagonal` argument is ignored in these 2 cases.
+- `correlate()` now works with single-column data.frames and numeric vectors (@antoine-sachet, #122). Note the `diagonal` argument is ignored in these 2 cases.
   
 - `network_plot()` now works with `cor_df` objects with only 1 or 2 columns (@antoine-sachet, #122)
 
diff --git a/man/corrr-package.Rd b/man/corrr-package.Rd
index 26204c3..bfd5a5a 100644
--- a/man/corrr-package.Rd
+++ b/man/corrr-package.Rd
@@ -33,10 +33,5 @@ Authors:
   \item Jorge Cimentada
 }
 
-Other contributors:
-\itemize{
-  \item Sachet Antoine \email{antoine.sac@gmail.com} [contributor]
-}
-
 }
 \keyword{internal}