Merge pull request #5 from maize-genetics/fix-plot-dot-evaluation

btmonier · web-flow · commit 10da0bb7bcec · 2024-04-02T15:52:39.000-05:00
Fix variable evaluation
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rPHG
-Version: 0.2.2
+Version: 0.2.3
 Date: 2019-06-03
 Title: R front-end for the practical haplotype graph
 Authors@R: c(
diff --git a/NEWS b/NEWS
@@ -1,3 +1,7 @@
+## CHANGES IN 0.2.3
+* Fixed issue with variable evaluation in the `plotDot()` function
+
+
 ## CHANGES IN VERSION 0.2.2
 * Fixed issue with `DEMO` method endpoint returning incorrect dimensional data
   for specific Maize PHGv1 methods
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+## rPHG 0.2.3
+* Fixed issue with variable evaluation in the `plotDot()` function
+
+
 ## rPHG 0.2.2
 * Fixed issue with `DEMO` method endpoint returning incorrect dimensional data
   for specific Maize PHGv1 methods
diff --git a/R/vis_plot_dot.R b/R/vis_plot_dot.R
@@ -30,6 +30,8 @@
 #' @importFrom ggplot2 scale_y_continuous
 #' @importFrom ggplot2 xlab
 #' @importFrom ggplot2 ylab
+#' @importFrom rlang sym
+#' @importFrom utils read.table
 #'
 #' @export
 plotDot <- function(
@@ -67,16 +69,16 @@ plotDot <- function(
 
     p <- ggplot2::ggplot(data = tmpData) +
         ggplot2::aes(
-            x = rlang::.data[["queryStart"]],
-            y = rlang::.data[["referenceStart"]],
-            color = rlang::.data[[colorId]]
+            x = !!rlang::sym("queryStart"),
+            y = !!rlang::sym("referenceStart"),
+            color = !!rlang::sym(colorId)
         ) +
         ggplot2::geom_point(size = 0.3) +
         ggplot2::scale_y_continuous(labels = toMb) +
         ggplot2::scale_x_continuous(labels = toMb) +
         ggplot2::facet_grid(
-            rows   = ggplot2::vars(rlang::.data[["refChr"]]),
-            col    = ggplot2::vars(rlang::.data[["queryChr"]]),
+            rows   = ggplot2::vars(!!rlang::sym("refChr")),
+            col    = ggplot2::vars(!!rlang::sym("queryChr")),
             scales = "free",
             space  = "free"
         ) +
diff --git a/inst/extdata/dummy_anchors_small.anchorspro b/inst/extdata/dummy_anchors_small.anchorspro
@@ -55,11 +55,6 @@ refChr	referenceStart	referenceEnd	queryChr	queryStart	queryEnd	strand	gene	bloc
 1	7665143	7665337	1	7062662	7062856	+	KXG37627	11	1
 1	7982452	7995826	1	7310024	7323534	+	interanchor	11	NA
 1	8052519	8060008	1	7385457	7392956	+	KXG37652	11	1
-1	8346617	8347468	scaffold125	212903	213771	-	OQU91078	54	1
-1	8348213	8368736	scaffold125	191281	212161	-	interanchor	54	NA
-1	8529688	8530695	scaffold125	39802	40809	-	EER90964	54	1
-1	8562187	8562798	scaffold125	11722	12333	-	EER90966	54	1
-1	8562799	8565062	scaffold125	9459	11721	-	interanchor	54	NA
 1	8683564	8730178	1	7513937	7620334	+	interanchor	34	NA
 1	8773501	8778922	1	7666507	7671910	+	interanchor	34	NA
 1	8838447	8839403	1	7719599	7720555	+	OQU91096	34	1
@@ -108,11 +103,6 @@ refChr	referenceStart	referenceEnd	queryChr	queryStart	queryEnd	strand	gene	bloc
 1	15357152	15360489	1	13645077	13648414	+	EER91293	25	1
 1	15361208	15362633	1	13649133	13650558	+	interanchor	25	NA
 1	15705032	15721336	1	13960528	13976802	+	interanchor	25	NA
-1	15851558	15857034	scaffold602	250880	256491	-	EER91319	62	1
-1	15880734	15884868	scaffold602	224407	227964	-	interanchor	62	NA
-1	15921680	15922473	scaffold602	187383	188176	-	interanchor	62	NA
-1	16430413	16433427	scaffold602	139638	142653	-	OQU91476	62	1
-1	16594420	16597665	scaffold602	52440	55685	-	KXG38154	62	1
 1	16991469	16992513	1	14230596	14231628	+	interanchor	20	NA
 1	17028966	17029625	1	14281774	14282433	+	EER93927	20	1
 1	17120576	17127698	1	14404379	14411420	+	interanchor	20	NA
@@ -530,12 +520,6 @@ refChr	referenceStart	referenceEnd	queryChr	queryStart	queryEnd	strand	gene	bloc
 2	59913779	59914512	2	54030818	54031548	+	interanchor	23	NA
 2	60117311	60118743	2	54234225	54235657	+	EER98942	23	1
 2	60530919	60533691	2	54422773	54424708	+	interanchor	23	NA
-2	60660176	60667077	scaffold98	833775	840657	+	interanchor	53	NA
-2	60913178	60921388	scaffold98	1075176	1083847	+	interanchor	53	NA
-2	60923834	60934927	scaffold98	1086293	1097441	+	interanchor	53	NA
-2	61009925	61013339	scaffold98	1170771	1174192	+	interanchor	53	NA
-2	61023935	61025038	scaffold98	1184957	1186060	+	EER96807	53	0.994565
-2	61062655	61063713	scaffold98	1227314	1228372	+	EER98982	53	1
 2	61113897	61115033	2	54557810	54559088	+	OQU89590	37	0.998095
 2	61130491	61137724	2	54574901	54582093	+	interanchor	37	NA
 2	61362533	61388118	2	54810662	54823046	+	interanchor	37	NA
@@ -553,19 +537,6 @@ refChr	referenceStart	referenceEnd	queryChr	queryStart	queryEnd	strand	gene	bloc
 2	63196948	63217180	2	56300283	56305608	+	interanchor	37	NA
 2	63588581	63592243	2	56691970	56752422	+	interanchor	37	NA
 2	63592244	63592825	2	56752423	56753004	+	OQU89694	37	1
-2	63920282	63920775	scaffold132	29123	29616	+	interanchor	46	NA
-2	64182220	64186215	scaffold132	291127	295122	+	EER99139	46	1
-2	64212764	64213627	scaffold132	321598	322461	+	OQU89737	46	1
-2	64246597	64248326	scaffold132	355383	357112	+	interanchor	46	NA
-2	64258491	64260329	scaffold132	367277	369115	+	interanchor	46	NA
-2	64305682	64309113	scaffold132	414285	417716	+	EER99152	46	1
-2	64309114	64310934	scaffold132	417717	419536	+	interanchor	46	NA
-2	64531618	64536282	scaffold132	646593	651239	+	KXG35981	46	0.993683
-2	64562462	64566130	scaffold132	674221	677960	+	interanchor	46	NA
-2	64566377	64568123	scaffold132	678207	679958	+	interanchor	46	NA
-2	64700324	64703231	scaffold132	822059	824968	+	EER97032	46	1
-2	65040539	65043568	scaffold132	1116702	1119718	+	EER99194	73	0.992381
-2	65087829	65088158	scaffold132	1168909	1169241	+	interanchor	73	NA
 2	65234791	65236124	2	57014668	57016004	+	OQU89791	24	0.997004
 2	65566645	65572370	2	57321962	57327686	+	EER97077	24	1
 2	65804935	65805369	2	57565223	57588265	+	interanchor	24	NA
@@ -905,8 +876,6 @@ refChr	referenceStart	referenceEnd	queryChr	queryStart	queryEnd	strand	gene	bloc
 3	60247258	60250455	3	53912008	53915204	+	EES03474	13	1
 3	60590197	60591614	3	54223212	54224128	+	EES01328	13	1
 3	60719028	60723946	3	54364427	54369343	+	interanchor	13	NA
-3	60827058	60828482	scaffold806	101120	102544	-	KXG33213	65	1
-3	60880809	60884633	scaffold806	56893	60703	-	EES03497	65	1
 3	61560148	61562960	3	54949707	54952519	+	OQU87441	48	1
 3	61568029	61569612	3	54959112	54960695	+	KXG33274	48	1
 3	61940523	61957754	3	55463343	55480548	+	interanchor	22	NA
@@ -1005,4 +974,4 @@ refChr	referenceStart	referenceEnd	queryChr	queryStart	queryEnd	strand	gene	bloc
 3	73942926	73944637	3	67785712	67787423	+	EES04283	47	1
 3	74053336	74054426	3	67892447	67893537	+	EES02132	47	1
 3	74279335	74280194	3	68130482	68131341	+	OQU88274	47	0.744792
-#block end
+#block end
