From 51fb36014a5c9bc92f74c0e6fc7f18daeab9e260 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Fri, 6 Oct 2023 09:12:51 +0000 Subject: [PATCH] Built site for gggenomes: 0.9.9.9000@a34516f --- articles/emales.html | 2 +- pkgdown.yml | 2 +- reference/Rplot002.png | Bin 1011 -> 2027 bytes reference/geom_gene.html | 2 +- reference/pick.html | 11 +++++------ reference/shift-1.png | Bin 0 -> 9589 bytes reference/shift-2.png | Bin 0 -> 9589 bytes reference/shift.html | 10 ++-------- 8 files changed, 10 insertions(+), 17 deletions(-) create mode 100644 reference/shift-1.png create mode 100644 reference/shift-2.png diff --git a/articles/emales.html b/articles/emales.html index 7b61cda0..84de9314 100644 --- a/articles/emales.html +++ b/articles/emales.html @@ -91,7 +91,7 @@

From a few sequences to a complex map in minutes

Thomas Hackl

-

2023-06-16

+

2023-10-06

Source: vignettes/emales.Rmd diff --git a/pkgdown.yml b/pkgdown.yml index 71eda4b8..f7f4ff57 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: emales: emales.html gggenomes: gggenomes.html -last_built: 2023-06-16T10:06Z +last_built: 2023-10-06T09:10Z diff --git a/reference/Rplot002.png b/reference/Rplot002.png index 17a358060aed2a86950757bbd25c6f92c08c458f..34f90fbc998a0d77109be710624e480bad0b9072 100644 GIT binary patch literal 2027 zcmeAS@N?(olHy`uVBq!ia0y~yV0-|=9Be?5+AI5}0x7m6Z+90U4Fo@(ch>_c&H|6f zVg?3oArNM~bhqvg0|R@vr;B4q#hkY{Hwrd82(TP<*9cvtQvg zquF4zbQmoaM`Ueq;Ph9_@+Z>ZPUiha(fWhXb(epW9 iIT$LW>`|-GM*i}xBD31_8ukL~Y6eeNKbLh*2~7ZD*DhiJ literal 1011 zcmeAS@N?(olHy`uVBq!ia0y~yV0-|=9Be?5+AI5}0x7m6Z+90U4Fo@(ch>_c&H|6f zVg?3oArNM~bhqvg0|WD9PZ!6KiaBo&GBN^{G%5UFpXcEKVvd5*5Eu=C0SJK)8A6*F U7`aXvEC5;V>FVdQ&MBb@00SN#Z2$lO diff --git a/reference/geom_gene.html b/reference/geom_gene.html index f4d0b69f..c6ba7af5 100644 --- a/reference/geom_gene.html +++ b/reference/geom_gene.html @@ -241,7 +241,7 @@

Examples

#> No seqs provided, inferring seqs from feats #> Warning: Ignoring unknown aesthetics: yend #> Error in geom_text(aes(label = "geom_feat", x = -15, y = 0.9)): Problem while computing layer data. -#> ℹ Error occurred in the 2nd layer. +#> ℹ Error occurred in the 3rd layer. #> Caused by error in `unrowname()`: #> ! Can only remove rownames from <data.frame> and <matrix> objects diff --git a/reference/pick.html b/reference/pick.html index 1358cc54..2378d861 100644 --- a/reference/pick.html +++ b/reference/pick.html @@ -160,7 +160,7 @@

Examples

# Align sequences with and plot next to a phylogenetic tree library(patchwork) # arrange multiple plots library(ggtree) # plot phylogenetic trees -#> ggtree v3.8.0 For help: https://yulab-smu.top/treedata-book/ +#> ggtree v3.8.2 For help: https://yulab-smu.top/treedata-book/ #> #> If you use the ggtree package suite in published research, please cite #> the appropriate paper(s): @@ -175,11 +175,10 @@

Examples

#> visualization of richly annotated phylogenetic data. Molecular Biology #> and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166 #> -#> LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR -#> Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package -#> for phylogenetic tree input and output with richly annotated and -#> associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. -#> doi: 10.1093/molbev/msz240 +#> Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan +#> Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data +#> object for visualization of a phylogenetic tree and annotation data. +#> iMeta 2022, 1(4):e56. doi:10.1002/imt2.56 #> #> Attaching package: ‘ggtree’ #> The following object is masked from ‘package:gggenomes’: diff --git a/reference/shift-1.png b/reference/shift-1.png new file mode 100644 index 0000000000000000000000000000000000000000..b1ae62ad56c95bf87590c00d3bd2c1998eeda98f GIT binary patch literal 9589 zcmeAS@N?(olHy`uVBq!ia0y~yU~gbxU_QXX1{ArnHDxD|VoUONcLCBs@Y8vBJ&@uo z@Q5sCV32JGVaEQaA5$3^6c{{R978JRyt#Rh_ke=Hfen}bmfKBpaB}&^@-zMHnHsQu z1_qn=`(>fb1Cne85T-*5BM*cnkjTIcVYx^gfG`*YN0os>Vl+U&>0va5fP-N)%YcJn zv~Yj~!)W0!S~!g6h0(mgFj_B+)(Z@yZ6t6a7|jc#d0{j!K+?cyUKq^_qj_O8FN}^O zQ9RPPd#?4dUI7j!g${qdi4K4Md+uR9$bR7A(}KpU;Zys|K3(H;Xkmcaq6i<)rakwz z-Bxa}2*ZK!=xM1Hd*A(k{CDTN*SoB1WR4r0|NQniBSgC5_V?Nu%U*ulBYXiOz#!P~ z=g|MyV$JJcD`TNT`)*nE^*@uJ+W=a<1OyNM7cfadmfb1Cne85T-*5BM*cnkjTIcVYx^gfG`*YN0os>Vl+U&>0va5fP-N)%YcJn zv~Yj~!)W0!S~!g6h0(mgFj_B+)(Z@yZ6t6a7|jc#d0{j!K+?cyUKq^_qj_O8FN}^O zQ9RPPd#?4dUI7j!g${qdi4K4Md+uR9$bR7A(}KpU;Zys|K3(H;Xkmcaq6i<)rakwz z-Bxa}2*ZK!=xM1Hd*A(k{CDTN*SoB1WR4r0|NQniBSgC5_V?Nu%U*ulBYXiOz#!P~ z=g|MyV$JJcD`TNT`)*nE^*@uJ+W=a<1OyNM7cfadmExamples # All bins have been shifted 10000 basepaiers gggenomes(seqs = emale_seqs) |> shift(bins = everything(), by = 10000) -#> Error in geom_blank(): Problem while computing layer data. -#> ℹ Error occurred in the 1st layer. -#> Caused by error in `unrowname()`: -#> ! Can only remove rownames from <data.frame> and <matrix> objects + geom_seq() + geom_bin_label() #> Error in eval(expr, envir, enclos): Cannot add <ggproto> objects together @@ -106,10 +103,7 @@

Examples

# Only RCC970_016B bin has been shifted for 5000 basepaiers gggenomes(seqs = emale_seqs) |> shift(bins = RCC970_016B, by = 5000, center = FALSE) -#> Error in geom_blank(): Problem while computing layer data. -#> ℹ Error occurred in the 1st layer. -#> Caused by error in `unrowname()`: -#> ! Can only remove rownames from <data.frame> and <matrix> objects + geom_seq() + geom_bin_label() #> Error in eval(expr, envir, enclos): Cannot add <ggproto> objects together