-
Notifications
You must be signed in to change notification settings - Fork 0
/
Plots.Rmd
60 lines (56 loc) · 2.27 KB
/
Plots.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
---
title: "R Notebook"
output: html_notebook
---
```{r}
data = read.csv("/Users/lazzataibekova/Dropbox (OIST)/varroa microbiome/DE_varroa_microbiome.csv")
data
```
###Varroa vs Microbiome
```{r}
plot(data$V_DE, data$M_DE, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Total number of DEG")
cor(data$V_DE, data$M_DE)
```
#Up-regulated genes
```{r}
plot(data$V_up.regulated, data$M_up.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of up-regulated genes")
cor(data$V_up.regulated, data$M_up.regulated)
```
#Down-regulated
```{r}
plot(data$V_down.regulated, data$M_down.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of down-regulated genes")
cor(data$V_down.regulated, data$M_down.regulated)
```
###Re-mapped Varroa vs Microbiome
```{r}
plot(data$V2_DE, data$M_DE, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Total number of DEG (re-mapped)")
cor(data$V2_DE, data$M_DE)
```
#Up-regulated genes
```{r}
plot(data$V2_up.regulated, data$M_up.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of up-regulated genes (re-mapped)")
cor(data$V2_up.regulated, data$M_up.regulated)
```
#Down-regulated genes
```{r}
plot(data$V2_down.regulated, data$M_down.regulated, xlab = "Varroa genes", ylab = "Microbiome genes", main = "Number of down-regulated genes (re-mapped)")
cor(data$V2_down.regulated, data$M_down.regulated)
```
###Gene-level analysis
```{r}
plot(data$V2_DE, data$V_gene_DE, xlab = "Re-mapped DE Varroa genes", ylab = "Gene-level DE VArroa", main = "Varroa DE vs Gene-level DE")
cor(data$V2_DE, data$V_gene_DE)
```
#Microbiome vs Varroa (gene-level)
```{r}
plot(data$V_gene_DE, data$M_DE, xlab = "Gene-level DE Varroa", ylab ="Microbiome DE", main = "Varroa Gene-level DE vs Microbiome DE")
cor(data$V_gene_DE, data$M_DE)
```
```{r}
plot(data$V_gene_up.regulated, data$M_up.regulated, xlab = "Gene-level up-regulated VArroa", ylab = "Microbiome up-regulated", main = "Varroa Gene-level vs Microbiome")
cor(data$V_gene_up.regulated, data$M_up.regulated)
```
```{r}
plot(data$V_gene_down.regulated, data$M_down.regulated, xlab = "Gene-level down-regulated VArroa", ylab = "Microbiome down-regulated", main = "Varroa Gene-level vs Microbiome")
cor(data$V_gene_down.regulated, data$M_down.regulated)
```