-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy path.Rhistory
215 lines (215 loc) · 10.3 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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
usethis::use_git()
usethis::use_git()
usethis::use_git()
usethis::use_git()
devtools::load_all(".")
usethis::use_mit_license("Alejandro Chibly")
usethis::use_mit_license("Alejandro Chibly")
devtools::document()
?LigandReceptorPairsTable
devtools::document()
devtools::document()
devtools::document()
document()
devtools::document()
use_readme_rmd()
usethis::use_readme_rmd()
install.packages("rmarkdown")
install.packages("rmarkdown")
usethis::use_readme_rmd()
devtools::load_all(".")
LRdatabase <- readxl::read_excel(path = "~/Desktop/testfile.xlsx")
names(LRdatabase) <- c("Pair", "Ligand", "Ligand.name", "Receptor", "Receptor.name")
LRdatabase$Pair <- tolower(LRdatabase$Pair)
LRdatabase$Pair <- Hmisc::capitalize(LRdatabase$Pair)
LRdatabase$Ligand <- tolower(LRdatabase$Ligand)
LRdatabase$Ligand <- Hmisc::capitalize(LRdatabase$Ligand)
LRdatabase$Receptor <- tolower(LRdatabase$Receptor)
LRdatabase$Receptor <- Hmisc::capitalize(LRdatabase$Receptor)
LRdatabase <- data.frame(lapply(LRdatabase, function(x) {
gsub("Ntf4", "Ntf5", x)
}))
View(LRdatabase)
test_dataset <- read.csv("~/Desktop/Test dataset.csv")
View(test_dataset)
test_dataset <- read.csv("~/Desktop/Test dataset.csv", row.names = 1)
View(test_dataset)
usethis::use_data(LRdatabase, test_dataset, internal = T)
devtools::build_readme()
devtools::build_readme()
View(test_dataset)
celltypelabels = as.vector(unique(test_dataset$cluster)) # create vector of cell identities
ncells = 23 #number of unique cell identities in SEURAT object
cellmarkers <- test_dataset # test_dataset obtained using FindAllMarkers from SEURAT
colors = topo.colors(ncells) # create vector of colors of length = ncells
## basic example code
library(Seurat)
library(LigandReceptor)
seuratDEGS <- test_dataset # test_dataset obtained using FindAllMarkers from SEURAT
ncells = 23 #number of unique cell identities in SEURAT object
celltypelabels = as.vector(unique(test_dataset$cluster)) # create vector of cell identities
colors = topo.colors(ncells) # create vector of colors of length = ncells
LRdatabase <- LRdatabase # Load ligand-receptor pair reference database
## This will generate a table with ligand-receptor pair for the specified cell types in celltypelabels
LR.pairs <- LigandReceptorPairsTable(ncells, celltypelabels, seuratDEGS, LRdatabase)
devtools::document()
## basic example code
library(Seurat)
library(LigandReceptor)
seuratDEGS <- test_dataset # test_dataset obtained using FindAllMarkers from SEURAT
ncells = 23 #number of unique cell identities in SEURAT object
celltypelabels = as.vector(unique(test_dataset$cluster)) # create vector of cell identities
colors = topo.colors(ncells) # create vector of colors of length = ncells
LRdatabase <- LRdatabase # Load ligand-receptor pair reference database
## This will generate a table with ligand-receptor pair for the specified cell types in celltypelabels
LR.pairs <- LigandReceptorPairsTable(ncells, celltypelabels, seuratDEGS, LRdatabase)
# This will generate the chord plot associated with the table
#PairsPlot <- function(filename, ncells, celltypelabels, cellcolors, seuratDEGS, LRdatabase, subsetgenes, from = celltypelabels, to = celltypelabels)
devtools::build_readme()
system.file("extdata", "test_dataset.csv", package = "LigandReceptor", mustWork = T)
write.csv(test_dataset, file = "~/Documents/MyGit/LigandReceptor/Inst/extdata/test_dataset.csv")
system.file("extdata", "test_dataset.csv", package = "LigandReceptor", mustWork = T)
write.csv(LRdatabase, file = "~/Documents/MyGit/LigandReceptor/Inst/extdata/LRdatabase.csv")
system.file("extdata", "LRdatabase.csv", package = "LigandReceptor", mustWork = T)
devtools::build_readme()
devtools::load_all(".")
devtools::build_readme()
usethis::use_data(LRdatabase, test_dataset, internal = T, overwrite = T)
devtools::build_readme()
devtools::document()
usethis::use_data_raw(LRdatabase, test_dataset, internal = T, overwrite = T)
usethis::use_data_raw(LRdatabase, test_dataset)
usethis::use_data_raw(name = "LRdatabase")
usethis::use_data("LRdatabase")
#'
#' @format A data frame with 2557 rows and 5 variables:
#' \describe{
#' \item{Pair}{Gene symbols of ligand-receptor pair}
#' \item{Ligand}{Gene symbol of Ligand}
#' \item{Ligand.name}{Gene name of ligand}
#' \item{Receptor}{Gene symbol of receptor}
#' \item{Receptor.name}{Gene name of receptor}
#' }
#' @source \url{https://static-content.springer.com/esm/art%3A10.1038%2Fncomms8866/MediaObjects/41467_2015_BFncomms8866_MOESM611_ESM.xlsx}
LRdatabase <- readxl::read_excel(path = "~/Desktop/testfile.xlsx")
names(LRdatabase) <- c("Pair", "Ligand", "Ligand.name", "Receptor", "Receptor.name")
LRdatabase$Pair <- tolower(LRdatabase$Pair)
LRdatabase$Pair <- Hmisc::capitalize(LRdatabase$Pair)
LRdatabase$Ligand <- tolower(LRdatabase$Ligand)
LRdatabase$Ligand <- Hmisc::capitalize(LRdatabase$Ligand)
LRdatabase$Receptor <- tolower(LRdatabase$Receptor)
LRdatabase$Receptor <- Hmisc::capitalize(LRdatabase$Receptor)
LRdatabase <- data.frame(lapply(LRdatabase, function(x) {
gsub("Ntf4", "Ntf5", x)
}))
"LRdatabase"
usethis::use_data("LRdatabase")
usethis::use_data_raw(name = "test_dataset")
usethis::use_data("test_dataset")
devtools::document()
usethis::use_data(test_dataset, internal = T, overwrite = T)
usethis::use_data(LRdatabase, internal = T, overwrite = T)
usethis::use_data(LRdatabase, test_dataset, internal = T, overwrite = T)
devtools::build_readme()
seuratDEGS <- LigandReceptor::LRdatabase #test_dataset obtained using FindAllMarkers from SEURAT
seuratDEGS <- LigandReceptor::test_dataset #test_dataset obtained using FindAllMarkers from SEURAT
devtools::build_readme()
usethis::use_data(test_dataset)
usethis::use_data(LRdatabase, test_dataset)
usethis::use_data(LRdatabase)
devtools::load_all(".")
devtools::build_readme()
devtools::document()
devtools::document()
devtools::document()
getwd()
usethis::use_data(LRdatabase)
usethis::use_data(LRdatabase, overwrite = T)
usethis::use_data(test_dataset, overwrite = T)
# This will generate the chord plot associated with the table
PairsPlot("filename.pdf", ncells, celltypelabels, cellcolors=colors, seuratDEGS, LRdatabase)
devtools::load_all(".")
## basic example code
library(Seurat)
library(LigandReceptor)
seuratDEGS <- LigandReceptor::test_dataset #test_dataset obtained using FindAllMarkers from SEURAT
ncells = 23 #number of unique cell identities in SEURAT object
celltypelabels = as.vector(unique(test_dataset$cluster)) # create vector of cell identities
colors = topo.colors(ncells) # create vector of colors of length = ncells
LRdatabase <- LigandReceptor::LRdatabase # Load ligand-receptor pair reference database
## This will generate a table with ligand-receptor pair for the specified cell types in celltypelabels
LR.pairs <- LigandReceptorPairsTable(ncells, celltypelabels, seuratDEGS, LRdatabase)
# This will generate the chord plot associated with the table
PairsPlot("filename.pdf", ncells, celltypelabels, cellcolors=colors, seuratDEGS, LRdatabase)
devtools::document()
## basic example code
library(Seurat)
library(LigandReceptor)
seuratDEGS <- LigandReceptor::test_dataset #test_dataset obtained using FindAllMarkers from SEURAT
ncells = 23 #number of unique cell identities in SEURAT object
celltypelabels = as.vector(unique(test_dataset$cluster)) # create vector of cell identities
colors = topo.colors(ncells) # create vector of colors of length = ncells
LRdatabase <- LigandReceptor::LRdatabase # Load ligand-receptor pair reference database
## This will generate a table with ligand-receptor pair for the specified cell types in celltypelabels
LR.pairs <- LigandReceptorPairsTable(ncells, celltypelabels, seuratDEGS, LRdatabase)
# This will generate the chord plot associated with the table
PairsPlot("filename.pdf", ncells, celltypelabels, cellcolors=colors, seuratDEGS, LRdatabase)
devtools::document()
devtools::load_all(".")
devtools::load_all(".")
## basic example code
library(Seurat)
library(LigandReceptor)
seuratDEGS <- LigandReceptor::test_dataset #test_dataset obtained using FindAllMarkers from SEURAT
ncells = 23 #number of unique cell identities in SEURAT object
celltypelabels = as.vector(unique(test_dataset$cluster)) # create vector of cell identities
colors = topo.colors(ncells) # create vector of colors of length = ncells
LRdatabase <- LigandReceptor::LRdatabase # Load ligand-receptor pair reference database
## This will generate a table with ligand-receptor pair for the specified cell types in celltypelabels
LR.pairs <- LigandReceptorPairsTable(ncells, celltypelabels, seuratDEGS, LRdatabase)
# This will generate the chord plot associated with the table
PairsPlot("filename.pdf", ncells, celltypelabels, cellcolors=colors, seuratDEGS, LRdatabase)
## basic example code
library(Seurat)
library(LigandReceptor)
seuratDEGS <- LigandReceptor::test_dataset #test_dataset obtained using FindAllMarkers from SEURAT
ncells = 23 #number of unique cell identities in SEURAT object
celltypelabels = as.vector(unique(test_dataset$cluster)) # create vector of cell identities
colors = topo.colors(ncells) # create vector of colors of length = ncells
LRdatabase <- LigandReceptor::LRdatabase # Load ligand-receptor pair reference database
## This will generate a table with ligand-receptor pair for the specified cell types in celltypelabels
LR.pairs <- LigandReceptorPairsTable(ncells, celltypelabels, seuratDEGS, LRdatabase)
# This will generate the chord plot associated with the table
PairsPlot("filename.pdf", ncells, celltypelabels, cellcolors=colors, seuratDEGS, LRdatabase, from = "Myoepithelial")
head(LR.pairs[LR.pairs$from %in% "Myoepithelial", ])
devtools::build_readme()
usethis::use_data(test_dataset, overwrite = T)
usethis::use_data(LRdatabase, overwrite = T)
library(LigandReceptor)
devtools::build_readme()
devtools::document()
devtools::build_readme()
usethis::use_data_raw(name = "LRdatabase")
usethis::use_data(LRdatabase)
usethis::use_data(LRdatabase, overwrite = T)
usethis::use_data(test_dataset, overwrite = T)
devtools::document()
devtools::build_readme()
library(LigandReceptor)
library(readr)
test_dataset <- read_csv("data-raw/Inst/extdata/test_dataset.csv")
View(test_dataset)
View(test_dataset)
rownames(test_dataset) <- test_dataset[,1]
rownames(test_dataset) <- test_dataset[1]
rownames(test_dataset) <- test_dataset$X1
View(test_dataset)
test_dataset <- test_dataset[,-1]
View(test_dataset)
unique(test_dataset$cluster)
count(unique(test_dataset$cluster))
sum(unique(test_dataset$cluster))
length(unique(test_dataset$cluster))
celltypelabels <- unique(test_dataset$cluster)
devtools::document()
devtools::document()