forked from kkdey/ecostructure
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path.Rhistory
178 lines (178 loc) · 6.56 KB
/
.Rhistory
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
devtools::document()
library(devtools)
install.packages("devtools")
library(devtools)
devtools::document()
devtools::document()
install.packages("ggplot2)
install.packages("ggplot2")
devtools::install_github("kkdey/Countclust")
library(maptpx)
library(ordtpx)
install_github("kkdey/ordtpx")
library(raster)
install.packages("raster")
devtools::document()
install.packages("rgdal")
library(utils)
library(grid)
library(gridExtra)
install.packages("gridExtra")
devtools::document()
packrat::restore(prompt = FALSE)
source('~/Documents/ecostructure/R/BlockStructure.R')
library(HimalayanBirdsAbundance)
data("HimalayanBirdsAbundance")
library(Biobase)
new_counts <- t(exprs(HimalayanBirdsAbundance));
metadata <- pData(HimalayanBirdsAbundance);
elevation_metadata=metadata$Elevation;
east_west_dir = metadata$WorE;
topic_clus <- maptpx::topics(new_counts, K=2, tol=0.1)
omega <- topic_clus$omega
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
library(HimalayanBirdsAbundance)
library(HimalayanBirdsAbundance)
install_github("kkdey/HimalayanBirdsAbundance")
library(devtools)
install_github("kkdey/HimalayanBirdsAbundance")
install_github("kkdey/HimalayanBirdsAbundance",
auth_token = "6276110c0334e1430b6cee2e706fea9c5f110d53")
library(HimalayanBirdsAbundance)
data("HimalayanBirdsAbundance")
library(Biobase)
new_counts <- t(exprs(HimalayanBirdsAbundance));
metadata <- pData(HimalayanBirdsAbundance);
elevation_metadata=metadata$Elevation;
east_west_dir = metadata$WorE;
topic_clus <- maptpx::topics(new_counts, K=2, tol=0.1)
omega <- topic_clus$omega
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
library(ecostructure)
library(gridExtra)
library(grid)
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
library(HimalayanBirdsAbundance)
data("HimalayanBirdsAbundance")
library(Biobase)
new_counts <- t(exprs(HimalayanBirdsAbundance));
metadata <- pData(HimalayanBirdsAbundance);
elevation_metadata=metadata$Elevation;
east_west_dir = metadata$WorE;
topic_clus <- maptpx::topics(new_counts, K=2, tol=0.1)
omega <- topic_clus$omega
library(gridExtra)
library(grid)
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
source('~/Documents/ecostructure/R/BlockStructure.R')
library(HimalayanBirdsAbundance)
data("HimalayanBirdsAbundance")
library(Biobase)
new_counts <- t(exprs(HimalayanBirdsAbundance));
metadata <- pData(HimalayanBirdsAbundance);
elevation_metadata=metadata$Elevation;
east_west_dir = metadata$WorE;
topic_clus <- maptpx::topics(new_counts, K=2, tol=0.1)
omega <- topic_clus$omega
library(gridExtra)
library(grid)
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
source('~/Documents/ecostructure/R/BlockStructure.R')
library(HimalayanBirdsAbundance)
data("HimalayanBirdsAbundance")
library(Biobase)
new_counts <- t(exprs(HimalayanBirdsAbundance));
metadata <- pData(HimalayanBirdsAbundance);
elevation_metadata=metadata$Elevation;
east_west_dir = metadata$WorE;
topic_clus <- maptpx::topics(new_counts, K=2, tol=0.1)
omega <- topic_clus$omega
library(gridExtra)
library(grid)
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
source('~/Documents/ecostructure/R/BlockStructure.R')
library(HimalayanBirdsAbundance)
data("HimalayanBirdsAbundance")
library(Biobase)
new_counts <- t(exprs(HimalayanBirdsAbundance));
metadata <- pData(HimalayanBirdsAbundance);
elevation_metadata=metadata$Elevation;
east_west_dir = metadata$WorE;
topic_clus <- maptpx::topics(new_counts, K=2, tol=0.1)
omega <- topic_clus$omega
library(gridExtra)
library(grid)
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
library(HimalayanBirdsAbundance)
data("HimalayanBirdsAbundance")
library(Biobase)
new_counts <- t(exprs(HimalayanBirdsAbundance));
metadata <- pData(HimalayanBirdsAbundance);
elevation_metadata=metadata$Elevation;
east_west_dir = metadata$WorE;
topic_clus <- maptpx::topics(new_counts, K=2, tol=0.000001)
omega <- topic_clus$omega
library(gridExtra)
library(grid)
BlockStructure(omega, blocker_metadata = east_west_dir,
order_metadata = elevation_metadata,
yaxis_label = "Elevation",
levels_decreasing = FALSE)
annotation = data.frame(x_names = c(paste0("A",1:5), paste0("B",1:5)),
x = c(0.5,2.0, 3.2, 4.6, 6.3, 23.5, 26.4, 28.5, 29.6, 31.8),
y1 = c(0.4, 0.3, 0.4, 0.35, 0.4, 0.8, 0.85, 0.9, 0.8, 0.75),
y2d =c(5, 6.6, 4, 5.2, 20, 3.4, 5.6, 4.5, 8, 10))
TopicMetaDiversity(annotation)
#' @title A bi-Y plot of topic proportions and a distance metric across sites, ordered by a metadata
source('~/Documents/ecostructure/R/TopicMetaDiversity.R')
annotation = data.frame(x_names = c(paste0("A",1:5), paste0("B",1:5)),
x = c(0.5,2.0, 3.2, 4.6, 6.3, 23.5, 26.4, 28.5, 29.6, 31.8),
y1 = c(0.4, 0.3, 0.4, 0.35, 0.4, 0.8, 0.85, 0.9, 0.8, 0.75),
y2d =c(5, 6.6, 4, 5.2, 20, 3.4, 5.6, 4.5, 8, 10))
TopicMetaDiversity(annotation)
source('~/Documents/ecostructure/R/TopicMetaMeta.R')
annotation = data.frame(x_names = c(paste0("A",1:5), paste0("B",1:5)),
x = c(0.5,2.0, 3.2, 4.6, 6.3, 23.5, 26.4, 28.5, 29.6, 31.8),
y1 = c(0.4, 0.3, 0.4, 0.35, 0.4, 0.8, 0.85, 0.9, 0.8, 0.75),
y2 =c(5, 6.6, 4, 5.2, 20, 3.4, 5.6, 4.5, 8, 10))
TopicMetaMeta(annotation)
source('~/Documents/ecostructure/R/TopicMetaMeta.R')
annotation = data.frame(x_names = c(paste0("A",1:5), paste0("B",1:5)),
x = c(0.5,2.0, 3.2, 4.6, 6.3, 23.5, 26.4, 28.5, 29.6, 31.8),
y1 = c(0.4, 0.3, 0.4, 0.35, 0.4, 0.8, 0.85, 0.9, 0.8, 0.75),
y2 =c(5, 6.6, 4, 5.2, 20, 3.4, 5.6, 4.5, 8, 10))
TopicMetaMeta(annotation)
source('~/Documents/ecostructure/R/TopicMetaMeta.R')
annotation = data.frame(x_names = c(paste0("A",1:5), paste0("B",1:5)),
x = c(0.5,2.0, 3.2, 4.6, 6.3, 23.5, 26.4, 28.5, 29.6, 31.8),
y1 = c(0.4, 0.3, 0.4, 0.35, 0.4, 0.8, 0.85, 0.9, 0.8, 0.75),
y2 =c(5, 6.6, 4, 5.2, 20, 3.4, 5.6, 4.5, 8, 10))
TopicMetaMeta(annotation)
source('~/Documents/ecostructure/R/TopicMetaMeta.R')
annotation = data.frame(x_names = c(paste0("A",1:5), paste0("B",1:5)),
x = c(0.5,2.0, 3.2, 4.6, 6.3, 23.5, 26.4, 28.5, 29.6, 31.8),
y1 = c(0.4, 0.3, 0.4, 0.35, 0.4, 0.8, 0.85, 0.9, 0.8, 0.75),
y2 =c(5, 6.6, 4, 5.2, 20, 3.4, 5.6, 4.5, 8, 10))
TopicMetaMeta(annotation)
install.packages("git2r")