enrichplot/NAMESPACE at devel · YuLab-SMU/enrichplot · GitHub

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
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
# Generated by roxygen2: do not edit by hand

S3method(as.data.frame,compareClusterResult)
S3method(barplot,compareClusterResult)
S3method(barplot,enrichResult)
S3method(cnetplot,compareClusterResult)
S3method(cnetplot,enrichResult)
S3method(cnetplot,gseaResult)
S3method(fortify,compareClusterResult)
S3method(fortify,enrichResult)
S3method(fortify,gseaResult)
S3method(ggplot_add,autofacet)
S3method(print,enrichplotDot)
export(autofacet)
export(cnetplot)
export(color_palette)
export(dotplot)
export(dotplot2)
export(emapplot)
export(facet_grid)
export(geneID)
export(geneInCategory)
export(geom_cnet_label)
export(geom_gsea_gene)
export(get_enrichplot_color)
export(ggtable)
export(ggtitle)
export(goplot)
export(gseaScores)
export(gseadist)
export(gseaplot)
export(gseaplot2)
export(gsearank)
export(heatplot)
export(hplot)
export(manhattanplot)
export(plot_list)
export(pmcplot)
export(ridgeplot)
export(set_enrichplot_color)
export(ssplot)
export(theme_dose)
export(treeplot)
export(upsetplot)
export(volplot)
exportMethods(dotplot)
exportMethods(emapplot)
exportMethods(goplot)
exportMethods(gseaplot)
exportMethods(heatplot)
exportMethods(manhattanplot)
exportMethods(pairwise_termsim)
exportMethods(ridgeplot)
exportMethods(ssplot)
exportMethods(treeplot)
exportMethods(upsetplot)
exportMethods(volplot)
import(GOSemSim)
importClassesFrom(enrichit,compareClusterResult)
importFrom(DOSE,theme_dose)
importFrom(RColorBrewer,brewer.pal)
importFrom(aplot,plot_list)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,desc)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,slice_head)
importFrom(dplyr,ungroup)
importFrom(enrichit,geneID)
importFrom(enrichit,geneInCategory)
importFrom(enrichit,gseaScores)
importFrom(ggfun,"%<+%")
importFrom(ggnewscale,new_scale_colour)
importFrom(ggnewscale,new_scale_fill)
importFrom(ggplot2,"%+%")
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,coord_equal)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,fortify)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_blank)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_linerange)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,ggplot_add)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,rel)
importFrom(ggplot2,scale_color_continuous)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,scale_fill_discrete)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_reverse)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(ggtangle,cnetplot)
importFrom(ggtangle,geom_cnet_label)
importFrom(ggtangle,geom_edge)
importFrom(ggtree,geom_cladelab)
importFrom(ggtree,geom_hilight)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,geom_tippoint)
importFrom(ggtree,ggtree)
importFrom(ggtree,gheatmap)
importFrom(ggtree,groupClade)
importFrom(graphics,barplot)
importFrom(grid,arrow)
importFrom(grid,gpar)
importFrom(grid,unit)
importFrom(igraph,'E<-')
importFrom(igraph,'V<-')
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,add_vertices)
importFrom(igraph,delete.edges)
importFrom(igraph,graph.empty)
importFrom(igraph,graph_from_data_frame)
importFrom(methods,is)
importFrom(methods,setGeneric)
importFrom(methods,setOldClass)
importFrom(purrr,map_df)
importFrom(rlang,.data)
importFrom(rlang,check_installed)
importFrom(rlang,sym)
importFrom(scatterpie,geom_scatterpie)
importFrom(scatterpie,geom_scatterpie_legend)
importFrom(stats,as.dist)
importFrom(stats,cutree)
importFrom(stats,hclust)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(tidydr,theme_dr)
importFrom(utils,data)
importFrom(utils,getFromNamespace)
importFrom(utils,head)
importFrom(utils,modifyList)
importFrom(yulab.utils,check_input)
importFrom(yulab.utils,get_cache_item)
importFrom(yulab.utils,str_wrap)
importFrom(yulab.utils,yulab_abort)
importFrom(yulab.utils,yulab_msg)
importFrom(yulab.utils,yulab_warn)