forked from YuLab-SMU/treedata-book
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathA-app-fig-tab.Rmd
145 lines (122 loc) · 6.76 KB
/
A-app-fig-tab.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
# Figures and Tables
```{r facet-geom, echo=FALSE,results='asis'}
x <- "ggalt\tgeom_dumbbell\tcreates dumbbell charts\n
ggbio\tgeom_alignment\tshows interval data as alignment\n
ggfittext\tgeom_fit_text\tshrinks, grows or wraps text to fit inside a defined rectangular area\n
gggenes\tgeom_gene_arrow\tdraws genes as arrows\n
ggimage\tgeom_image\tvisualizes image files\n
ggimage\tgeom_phylopic\tqueries image files from phylopic database and visualizes them\n
ggplot2\tgeom_hline\tadds horizontal lines\n
ggplot2\tgeom_jitter\tadds a small amount of random variation to the location of each point\n
ggplot2\tgeom_label\tdraws a rectangle behind the text\n
ggplot2\tgeom_point\tcreats scatterplots\n
ggplot2\tgeom_raster\ta high performance special case for all the tiles are the same size\n
ggplot2\tgeom_rect\tdraws rectangle by using the locations of the four coners\n
ggplot2\tgeom_segment\tdraws a straight line between points\n
ggplot2\tgeom_spoke\ta polar parameterisation of 'geom_segment()'\n
ggplot2\tgeom_text\tadds text to the plot\n
ggplot2\tgeom_tile\tdraws rectangle by using the center of the tile and its size\n
ggplot2\tgeom_vline\tadds vertical lines\n
ggrepel\tgeom_text_repel\tadds text to the plot. The text labels repel away from each other and away from the data points\n
ggrepel\tgeom_label_repel\tdraws a rectangle underneath the text. The text labels repel away from each other and away from the data ponts\n
ggridges\tgeom_density_ridges\tarranges multiple density plots in a staggered fashion\n
ggridges\tgeom_density_ridges_gradient\tworks just like 'geom_density_ridges' except that the 'fill' aesthetic can vary along the x axis\n
ggridges\tgeom_ridgeline\tplots the sum of the 'y' and 'height' aesthetics versus 'x', filling the area between 'y' and 'y + height' with a color\n
ggridges\tgeom_ridgeline_gradient\tworks just like 'geom_ridgeline' except that the 'fill' aesthetic can vary along the x axis\n
ggstance\tgeom_barh\thorizontal version of 'geom_bar()'\n
ggstance\tgeom_boxploth\thorizontal version of 'geom_boxplot()'\n
ggstance\tgeom_crossbarh\thorizontal version of 'geom_crossbar()'\n
ggstance\tgeom_errorbarh\thorizontal version of 'geom_errorbarh()'\n
ggstance\tgeom_histogramh\thorizontal version of 'geom_histogram()'\n
ggstance\tgeom_linerangeh\thorizontal version of 'geom_linerange()'\n
ggstance\tgeom_pointrangeh\thorizontal version of 'geom_pointrange()'\n
ggstance\tgeom_violinh\thorizontal version of 'geom_violin()'\n
ggtree\tgeom_motif\tdraws aligned motifs\n
"
xx <- strsplit(x, "\n\n")[[1]]
y <- strsplit(xx, "\t") %>% do.call("rbind", .)
y <- as.data.frame(y)
colnames(y) <- c("Package", "Geom Layer", "Description")
require(kableExtra)
caption = "Geometric layers that supported by 'geom_facet()' and 'facet_plot()'"
knitr::kable(y, caption=caption, booktabs = T) %>%
collapse_rows(columns = 1, latex_hline = "major", valign ="top") %>%
kable_styling(latex_options = c("striped", "scale_down"),
bootstrap_options = c("striped", "hover")) #%>% landscape
```
```{r tree-objects, echo=FALSE,results='asis'}
x <- tibble::tribble(
~Package, ~Object, ~Description,
"ape", "phylo", "basic phylogenetic tree structure",
"ape", "multiPhylo", "list of phylo objects",
"ade4", "phylog", "tree structure for ecological data",
"phylobase", "phylo4", "S4 version of phylo object",
"phylobase", "phylo4d", "extend phylo4 with trait data",
"phyloseq", "phyloseq", "phylogenetic tree with microbiome data",
"tidytree", "tbl_tree", "phylogenetic tree as a tidy data frame",
"treeio", "treedata", "phylogenetic tree with heterogeneous associated data",
"treeio", "jplace", "treedata object with placement information",
"stats", "hclust", "hierarchical cluster result",
"stats", "dendrogram", "hierarchical clustering or classification/regression tree",
"cluster", "agnes", "agglomerative hierarchical clustering",
"cluster", "diana", "divisive hierarchical clustering",
"cluster", "twins", "agglomerative or divisive (polythetic) hierarchical clustering",
"pvclust", "pvclust", "hierarchical clustering with p-values calculated by multiscale bootstrap resampling",
"igraph", "igraph", "network (currently only tree graph supportted)"
)
y <- as.data.frame(x)
require(kableExtra)
caption = "Tree-like objects supported by ggtree"
knitr::kable(y, caption=caption, booktabs = T) %>%
collapse_rows(columns = 1, latex_hline = "major", valign ="top") %>%
kable_styling(latex_options = c("striped", "scale_down"),
bootstrap_options = c("striped", "hover")) #%>% landscape
```
<!--
#``` r treeio, echo=F, message=FALSE}
library(kableExtra)
ff <- matrix(c(
'read.beast', "parsing output of BEAST",
"read.codeml", "parsing output of CodeML (rst and mlc files)",
"read.codeml_mlc", "parsing mlc file (output of CodeML)",
"read.hyphy", "parsing output of HYPHY",
"read.jplace", "parsing jplace file including output of EPA and pplacer",
"read.nhx", "parsing NHX file including output of PHYLDOG and RevBayes",
"read.paml_rst", "parsing rst file (output of BaseML or CodeML)",
"read.phylip", "parsing phylip file",
"read.phyloT", "parsing output of phyloT (http://phylot.biobyte.de/)",
"read.r8s", "parsing output of r8s",
"read.raxml", "parsing output of RAxML",
"Nnode", "get number of internal nodes",
"Nnode2", "get number of all nodes (including internal and external nodes)",
"Ntip", "get number of all tips (external nodes)",
"as.phylo", "convert tree object to phylo object",
"as.treedata", "convert tree object to treedata object",
"drop.tip", "remove tips in a tree",
"get.fields", "get available tree attributes stored in tree object",
"get.placements", "get placement result of jplace object",
"get.subs", "get substitution by comparing parent node and child node",
"get.tipseq", "get tip sequences",
"get.treetext", "get newick text of a tree object",
"groupClade", "add clade grouping information to tree object",
"groupOTU", "grouping OTUs by tracing back to most recent commond ancestor",
"merge_tree", "merging tree objects into one",
"write.jpace", "write tree with associated annotation data to a jplace file"
), ncol=2, byrow=TRUE)
ff <- as.data.frame(ff)
colnames(ff) <- c("Function", "Description")
knitr::kable(ff, caption = "Functions defined in treeio.", booktabs = T) #%>%
#kable_styling(latex_options = c("striped", "hold_position"), full_width = T)
```
-->
# Session Info {#session-info}
The book was written using R Markdown and was compiled by `r CRANpkg("bookdown")` package. Here is the session information on the system on which this thesis was compiled:
```{r sessionInfo, echo=FALSE, cache=FALSE}
## options(width=90)
devtools::session_info()
if (FALSE) {
sessionInfo() %>% capture.output %>%
`[`(., -c(5:8)) %>% paste('\n') %>% cat
}
## options(width=80)
```