1. ggtree
  2. R
  3. zzz.R
Browse code

mv pillar

xiangpin authored on 07/03/2022 06:19:21
Showing 1 changed files
R/zzz.R
History View file @ 3ee701f2
... ... 
@@ -1,5 +1,4 @@
1 1 
 ##' @importFrom utils packageDescription
2 
-##' @importFrom pillar style_subtle
3 2 
 .onAttach <- function(libname, pkgname) {
4 3 
     pkgVersion <- packageDescription(pkgname, fields = "Version")
5 4 
     ref <- random_ref(pkgname = pkgname, pkgVersion = pkgVersion, random_n = 2)
Browse code

update the print of refs

xiangpin authored on 03/03/2022 03:22:04
Showing 1 changed files
R/zzz.R
History View file @ a653972a
... ... 
@@ -1,15 +1,9 @@
1 1 
 ##' @importFrom utils packageDescription
2 2 
 ##' @importFrom pillar style_subtle
3 3 
 .onAttach <- function(libname, pkgname) {
4 
-    pkgVersion <- packageDescription(pkgname, fields="Version")
5 
-    msg <- style_subtle(paste0(pkgname, " v", pkgVersion, "  ",
6 
-                  "For help: https://yulab-smu.top/treedata-book/", "\n\n"))
7 
-
8 
-    #citation <- paste0("If you use ", pkgname,
9 
-    #                   " in published research, please cite the most appropriate paper(s):\n\n",
10 
-    #                   ggtree_citations(), "\n")
11 
-    citation <- random_ref()
12 
-    packageStartupMessage(paste(strwrap(paste0(msg, citation)), collapse = "\n"))
4 
+    pkgVersion <- packageDescription(pkgname, fields = "Version")
5 
+    ref <- random_ref(pkgname = pkgname, pkgVersion = pkgVersion, random_n = 2)
6 
+    if (!is.null(ref)) packageStartupMessage(ref)
13 7 
 }
14 8
15 9 
 random_ref <- getFromNamespace("random_ref", 'tidytree')
Browse code

update citation

xiangpin authored on 01/03/2022 07:37:15
Showing 1 changed files
R/zzz.R
History View file @ f1d8298d
... ... 
@@ -1,14 +1,15 @@
1 1 
 ##' @importFrom utils packageDescription
2 
+##' @importFrom pillar style_subtle
2 3 
 .onAttach <- function(libname, pkgname) {
3 4 
     pkgVersion <- packageDescription(pkgname, fields="Version")
4 
-    msg <- paste0(pkgname, " v", pkgVersion, "  ",
5 
-                  "For help: https://yulab-smu.top/treedata-book/", "\n\n")
6 
-
7 
-    citation <- paste0("If you use ", pkgname,
8 
-                       " in published research, please cite the most appropriate paper(s):\n\n",
9 
-                       ggtree_citations(), "\n")
10 
-
11 
-    packageStartupMessage(paste0(msg, citation))
5 
+    msg <- style_subtle(paste0(pkgname, " v", pkgVersion, "  ",
6 
+                  "For help: https://yulab-smu.top/treedata-book/", "\n\n"))
7 
+
8 
+    #citation <- paste0("If you use ", pkgname,
9 
+    #                   " in published research, please cite the most appropriate paper(s):\n\n",
10 
+    #                   ggtree_citations(), "\n")
11 
+    citation <- random_ref()
12 
+    packageStartupMessage(paste(strwrap(paste0(msg, citation)), collapse = "\n"))
12 13 
 }
13 14
14 
-
15 
+random_ref <- getFromNamespace("random_ref", 'tidytree')
Browse code

update

Guangchuang Yu authored on 08/01/2021 07:30:55
Showing 1 changed files
R/zzz.R
History View file @ 7353eb90
... ... 
@@ -4,24 +4,11 @@
4 4 
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
5 5 
                   "For help: https://yulab-smu.top/treedata-book/", "\n\n")
6 6
7 
-    citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 
-
9 
-                       '\033[36m', '-', '\033[39m ',
10 
-                       "Guangchuang Yu. ",
11 
-                       "Using ggtree to visualize data on tree-like structures. ",
12 
-                       "Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96\n",
13 
-
14 
-                       '\033[36m', '-', '\033[39m ',
15 
-                       "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
16 
-                       "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
17 
-                       "Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194\n",
18 
-
19 
-                       '\033[36m', '-', '\033[39m ',
20 
-                       "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
21 
-                       "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
22 
-                       "Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628\n\n"
23 
-
24 
-                       )
7 
+    citation <- paste0("If you use ", pkgname,
8 
+                       " in published research, please cite the most appropriate paper(s):\n\n",
9 
+                       ggtree_citations(), "\n")
25 10
26 11 
     packageStartupMessage(paste0(msg, citation))
27 12 
 }
13 
+
14 
+
Browse code

update url

Guangchuang Yu authored on 13/11/2020 14:29:27
Showing 1 changed files
R/zzz.R
History View file @ 6c69186a
... ... 
@@ -2,7 +2,7 @@
2 2 
 .onAttach <- function(libname, pkgname) {
3 3 
     pkgVersion <- packageDescription(pkgname, fields="Version")
4 4 
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
5 
-                  "For help: https://yulab-smu.github.io/treedata-book/", "\n\n")
5 
+                  "For help: https://yulab-smu.top/treedata-book/", "\n\n")
6 6
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 8
Browse code

update citation

Guangchuang Yu authored on 25/03/2020 13:51:45
Showing 1 changed files
R/zzz.R
History View file @ ccc21786
... ... 
@@ -19,7 +19,7 @@
19 19 
                        '\033[36m', '-', '\033[39m ',
20 20 
                        "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
21 21 
                        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
22 
-                       "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n"
22 
+                       "Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628\n\n"
23 23
24 24 
                        )
25 25
Browse code

new citation

Guangchuang Yu authored on 19/03/2020 13:18:33
Showing 1 changed files
R/zzz.R
History View file @ f9c9f2f8
... ... 
@@ -5,6 +5,12 @@
5 5 
                   "For help: https://yulab-smu.github.io/treedata-book/", "\n\n")
6 6
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 
+
9 
+                       '\033[36m', '-', '\033[39m ',
10 
+                       "Guangchuang Yu. ",
11 
+                       "Using ggtree to visualize data on tree-like structures. ",
12 
+                       "Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96\n",
13 
+
8 14 
                        '\033[36m', '-', '\033[39m ',
9 15 
                        "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
10 16 
                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
... ... 
@@ -14,6 +20,7 @@
14 20 
                        "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
15 21 
                        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
16 22 
                        "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n"
23 
+
17 24 
                        )
18 25
19 26 
     packageStartupMessage(paste0(msg, citation))
Browse code

rm space

Guangchuang Yu authored on 19/03/2020 07:10:04
Showing 1 changed files
R/zzz.R
History View file @ 56752aa0
... ... 
@@ -8,7 +8,7 @@
8 8 
                        '\033[36m', '-', '\033[39m ',
9 9 
                        "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
10 10 
                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
11 
-                       "Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194\n",
11 
+                       "Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194\n",
12 12
13 13 
                        '\033[36m', '-', '\033[39m ',
14 14 
                        "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
Browse code

update citation

Guangchuang Yu authored on 26/08/2019 10:19:27
Showing 1 changed files
R/zzz.R
History View file @ 27e7a82e
... ... 
@@ -8,7 +8,7 @@
8 8 
                        '\033[36m', '-', '\033[39m ',
9 9 
                        "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
10 10 
                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
11 
-                       "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194",
11 
+                       "Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194\n",
12 12
13 13 
                        '\033[36m', '-', '\033[39m ',
14 14 
                        "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
Browse code

update url

Guangchuang Yu authored on 28/05/2019 10:24:48
Showing 1 changed files
R/zzz.R
History View file @ 3fbeced3
... ... 
@@ -2,7 +2,7 @@
2 2 
 .onAttach <- function(libname, pkgname) {
3 3 
     pkgVersion <- packageDescription(pkgname, fields="Version")
4 4 
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
5 
-                  "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")
5 
+                  "For help: https://yulab-smu.github.io/treedata-book/", "\n\n")
6 6
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 8 
                        '\033[36m', '-', '\033[39m ',
Browse code

bug fixed for geom_hilight, in tidytree

Guangchuang Yu authored on 26/02/2019 09:16:33
Showing 1 changed files
R/zzz.R
History View file @ 7566a86d
... ... 
@@ -5,14 +5,15 @@
5 5 
                   "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")
6 6
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 
-                       '\033[36m', '-', '\033[39m ',
9 
-                       "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
10 
-                       "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
11 
-                       "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n",
12 8 
                        '\033[36m', '-', '\033[39m ',
13 9 
                        "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
14 10 
                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
15 
-                       "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194"
11 
+                       "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194",
12 
+
13 
+                       '\033[36m', '-', '\033[39m ',
14 
+                       "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
15 
+                       "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
16 
+                       "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n"
16 17 
                        )
17 18
18 19 
     packageStartupMessage(paste0(msg, citation))
Browse code

update docs

Guangchuang Yu authored on 19/11/2018 08:17:45
Showing 1 changed files
R/zzz.R
History View file @ e97f14c3
... ... 
@@ -5,11 +5,11 @@
5 5 
                   "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")
6 6
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 
-                       '\033[36m', '\u25C9', '\033[39m ',
8 
+                       '\033[36m', '-', '\033[39m ',
9 9 
                        "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
10 10 
                        "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
11 11 
                        "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n",
12 
-                       '\033[36m', '\u25C9', '\033[39m ',
12 
+                       '\033[36m', '-', '\033[39m ',
13 13 
                        "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
14 14 
                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
15 15 
                        "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194"
Browse code

update citation

Guangchuang Yu authored on 24/10/2018 08:49:10
Showing 1 changed files
R/zzz.R
History View file @ 76dd59a1
... ... 
@@ -5,13 +5,15 @@
5 5 
                   "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")
6 6
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 
-                  "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
9 
-                  "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
10 
-                  "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n",
11 
-                  "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan.",
12 
-                  "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
13 
-                  "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194"
14 
-                  )
8 
+                       '\033[36m', '\u25C9', '\033[39m ',
9 
+                       "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
10 
+                       "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
11 
+                       "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n",
12 
+                       '\033[36m', '\u25C9', '\033[39m ',
13 
+                       "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ",
14 
+                       "Two methods for mapping and visualizing associated data on phylogeny using ggtree. ",
15 
+                       "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194"
16 
+                       )
15 17
16 18 
     packageStartupMessage(paste0(msg, citation))
17 19 
 }
Browse code

add citation

Guangchuang Yu authored on 24/10/2018 06:17:50
Showing 1 changed files
R/zzz.R
History View file @ 38554c25
... ... 
@@ -4,10 +4,14 @@
4 4 
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
5 5 
                   "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")
6 6
7 
-    citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
7 
+    citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",
8 8 
                   "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
9 9 
                   "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
10 
-                  "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628")
10 
+                  "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n",
11 
+                  "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan.",
12 
+                  "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",
13 
+                  "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194"
14 
+                  )
11 15
12 16 
     packageStartupMessage(paste0(msg, citation))
13 17 
 }
Browse code

fixed links

guangchuang yu authored on 12/03/2018 03:17:35
Showing 1 changed files
R/zzz.R
History View file @ 2ea8a3b5
... ... 
@@ -2,7 +2,7 @@
2 2 
 .onAttach <- function(libname, pkgname) {
3 3 
     pkgVersion <- packageDescription(pkgname, fields="Version")
4 4 
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
5 
-                  "For help: https://guangchuangyu.github.io/", pkgname, "\n\n")
5 
+                  "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")
6 6
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
8 8 
                   "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
Browse code

update citation

GuangchuangYu authored on 20/01/2017 05:21:52
Showing 1 changed files
R/zzz.R
History View file @ 6788b024
... ... 
@@ -7,7 +7,7 @@
7 7 
     citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
8 8 
                   "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
9 9 
                   "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
10 
-                  "Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628")
10 
+                  "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628")
11 11
12 12 
     packageStartupMessage(paste0(msg, citation))
13 13 
 }
Browse code

startup msg

guangchuang yu authored on 09/11/2016 07:54:06
Showing 1 changed files
R/zzz.R
History View file @ a51a4376
... ... 
@@ -1,4 +1,5 @@
1 
-.onLoad <- function(libname, pkgname) {
1 
+##' @importFrom utils packageDescription
2 
+.onAttach <- function(libname, pkgname) {
2 3 
     pkgVersion <- packageDescription(pkgname, fields="Version")
3 4 
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
4 5 
                   "For help: https://guangchuangyu.github.io/", pkgname, "\n\n")
Browse code

.onLoad

guangchuang yu authored on 09/11/2016 04:43:48
Showing 1 changed files
R/zzz.R
History View file @ 36b87ad2
... ... 
@@ -1,11 +1,12 @@
1 
-.onAttach <- function(libname, pkgname) {
1 
+.onLoad <- function(libname, pkgname) {
2 2 
     pkgVersion <- packageDescription(pkgname, fields="Version")
3 3 
     msg <- paste0(pkgname, " v", pkgVersion, "  ",
4 4 
                   "For help: https://guangchuangyu.github.io/", pkgname, "\n\n")
5 5
6 
-    citation <- paste0("If you use ", pkgnameg, " in published research, please cite:\n",
6 
+    citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
7 7 
                   "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
8 8 
                   "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
9 9 
                   "Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628")
10 
+
10 11 
     packageStartupMessage(paste0(msg, citation))
11 12 
 }
Browse code

startup msg

guangchuang yu authored on 09/11/2016 04:34:38
Showing 1 changed files
R/zzz.R
History View file @ c25bdbe6
... ... 
@@ -1,8 +1,11 @@
1 1 
 .onAttach <- function(libname, pkgname) {
2 
-    ##	pkgVersion <- packageDescription(pkgname, fields="Version")
3 
-    msg <- paste0("If you use ggtree in published research, please cite:\n\n",
4 
-                  "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.\n",
5 
-                  "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.\n",
6 
-                  "Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628\n\n")
7 
-    packageStartupMessage(msg)
2 
+    pkgVersion <- packageDescription(pkgname, fields="Version")
3 
+    msg <- paste0(pkgname, " v", pkgVersion, "  ",
4 
+                  "For help: https://guangchuangyu.github.io/", pkgname, "\n\n")
5 
+
6 
+    citation <- paste0("If you use ", pkgnameg, " in published research, please cite:\n",
7 
+                  "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
8 
+                  "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",
9 
+                  "Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628")
10 
+    packageStartupMessage(paste0(msg, citation))
8 11 
 }
Browse code

citation info with doi

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120192 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 17/08/2016 05:42:13
Showing 1 changed files
R/zzz.R
History View file @ 567ab02f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,8 @@
1 
+.onAttach <- function(libname, pkgname) {
2 
+    ##	pkgVersion <- packageDescription(pkgname, fields="Version")
3 
+    msg <- paste0("If you use ggtree in published research, please cite:\n\n",
4 
+                  "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.\n",
5 
+                  "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.\n",
6 
+                  "Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628\n\n")
7 
+    packageStartupMessage(msg)
8 
+}