-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path.Rhistory
132 lines (132 loc) · 3.77 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
library(roxygen2)
devtools::document()
devtools::document()
class()
devtools::document()
?setClass
?setOldClass
setOldClass("Seqinfo",S4Class)
setOldClass("Seqinfo","Seqinfo")
devtools::document()
?t.test
devtools::document()
devtools::document()
R CMD check results
devtools::check()
usethis::use_package()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
warnings()
devtools::document()
devtools::document()
warnings()
dplyr
devtools::document()
devtools::document()
library(dpylr)
library(dplyr)
devtools::document()
devtools::document()
devtools::document()
R CMD check results
devtools::check()
devtools::check()
devtools::document()
devtools::check()
?dir.create
file.exists("R")
file.exists("R/fagin.R")
devtools::document()
devtools::check()
devtools::document()
devtools::check()
devtools::document()
?set_rownames
devtools::document()
message("skip loading ", species, ", read rds instead")
species="b"
message("skip loading ", species, ", read rds instead")
focal="a"
target="b"
message("skip comparison for ", focal, " and ", target, ", read RDS instead")
devtools::document()
print("load species ",species)
print("load species ")
species="a"
print("load species ",species)
print(c("load species ",species))
print(paste0("load species ",species))
a <- list("a"="a","b"="b")
b <- list(a,"c"="c")
b
devtools::document()
install.packages("doParallel")
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
foreach
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
devtools::document()
stop("Query gene list not found")
species="a"
stop("Query gene list",species, "not found")
setwd("C:/Users/jingli/Box/research/arabidopsis/rice")
anno <- readRDS("anno.rds")
x <- read.table("pool.txt")
x <- read.table("upset/pool.txt")
x <- read.table("upset/pool/pool.txt")
head(x)
View(x)
x <- read.table("upset/pool/pool.txt",header=T)
sum(x$DirInf)
sum(x$Maker)
sum(x$NCBI)
sum(x$Braker)
sum(x$BIND)
sum(x$MIND)
all_wide <-read.table("figure2_ps.csv",header=T,sep=",")
setwd("C:/Users/jingli/Box/research/arabidopsis")
all_wide <-read.table("figure2_ps.csv",header=T,sep=",")
all_long <- gather(all_wide,Method,PC,MAKER_small:BIND_orphan,factor_key=TRUE)
library(tidyr)
library(ggplot2)
all_long <- gather(all_wide,Method,PC,MAKER_small:BIND_orphan,factor_key=TRUE)
all_long <- gather(all_wide,Method,PC,MAKER_Typical:BIND_Orphan,factor_key=TRUE)
View(all_long)
View(anno)
View(all_wide)
all_long$ps <- factor(all_long$ps, levels=c("Arabidopsis thaliana", "Arabidopsis", "Camelineae", "Brassicaceae", "Malvids", "Rosids", "Pentapetalae", "Mesangiospermae", "Magnoliophyta", "Tracheophyta", "Embryophyta", "Streptophytina", "Streptophyta", "Viridiplantae", "Eukaryota", "Cellular Organisms"))
ggplot(all_long, aes(x = ps, y = PC, fill = ps)) +
geom_bar(stat = "identity", position = "dodge") +
facet_wrap(ncol = 3, ~ Method) +
scale_fill_manual(values=c("#D4322F", "#B32DF5", "#F6C245", "#469CAE", "#2254D4", "#E46D2F", "#58C1F1", "#54308B", "#EE8948", "#3C8A43", "#A9C85E", "#53B634", "#D75AC9", "#7B17F4", "#2620D4", "#9D1D88")) +
coord_flip() +
ylim(0, 100) +
labs(x = "Phylostrata", y = "Percent genes matching Araport11 annotations") +
theme(axis.title.x=element_text(size=20),
axis.title.y=element_text(size=20),
legend.position = "none",
plot.title = element_text(hjust = 0.5, size=16),
axis.text.y = element_text(face = "italic", size=16),
axis.text.x = element_text(size=16),
strip.text = element_text(size = 14))
setwd("C:/Users/jingli/Box/research/fagin2")
setwd("C:/Users/jingli/github/fagin2/fagin2/R")
devtools::document()
devtools::document()
rev(c(1,4,5,34))
devtools::document()
devtools::document()