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Fix variable evaluation #5

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Apr 2, 2024
Merged

Fix variable evaluation #5

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -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(
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4 changes: 4 additions & 0 deletions NEWS
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@@ -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
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4 changes: 4 additions & 0 deletions NEWS.md
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@@ -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
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12 changes: 7 additions & 5 deletions R/vis_plot_dot.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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"
) +
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33 changes: 1 addition & 32 deletions inst/extdata/dummy_anchors_small.anchorspro
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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