Add files via upload

MikheyevLab · Jun 7, 2019 · 29617ee · 29617ee
1 parent 3889010
commit 29617ee
Show file tree

Hide file tree

Showing 7 changed files with 30,845 additions and 47 deletions.
diff --git a/DE_varroa.Rmd b/DE_varroa.Rmd
@@ -157,7 +157,7 @@ up_down_regulated
 ### Аrresting vs. pre-laying
 
 ```{r}
-so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "prelaying")), extra_bootstrap_summary = TRUE)
+so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("arresting", "prelaying")), extra_bootstrap_summary = TRUE)
 so <- sleuth_fit(so, ~condition, 'full')
 so <- sleuth_fit(so, ~1, 'reduced')
 so <- sleuth_lrt(so, 'reduced', 'full')
@@ -189,7 +189,7 @@ up_down_regulated
 ### Pre-laying vs. Laying
 
 ```{r}
-so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "laying")), extra_bootstrap_summary = TRUE)
+so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("prelaying", "laying")), extra_bootstrap_summary = TRUE)
 so <- sleuth_fit(so, ~condition, 'full')
 so <- sleuth_fit(so, ~1, 'reduced')
 so <- sleuth_lrt(so, 'reduced', 'full')
@@ -204,8 +204,8 @@ models(so)
 ```
 Number of Differentially expressed genes (TRUE):
 ```{r}
-so = sleuth_wt(so, 'conditionphoretic')
-results_table = sleuth_results(so, 'conditionphoretic')
+so = sleuth_wt(so, 'conditionprelaying')
+results_table = sleuth_results(so, 'conditionprelaying')
 Number_DE_genes = table(results_table$qval <= 0.05)
 Number_DE_genes
 ```

diff --git a/DE_varroa_microbiome.csv b/DE_varroa_microbiome.csv
@@ -1,13 +1,13 @@
-Stages,M_DE,M_up-regulated,M_down-regulated,V_DE,V_up-regulated,V_down-regulated,V2_DE,V2_up-regulated,V2_down-regulated
-males vs young,5397,1596,3801,19220,8328,10892,8069,2641,5428
-Young vs Phoretic,2852,1570,1282,12769,6846,5923,3374,1763,1611
-Phoretics vs caged,1,0,1,0,0,0,23,13,10
-Phoretic vs arresting,68,19,49,3514,1288,2226,100,36,64
-Arrest vs pre-laying,2866,1527,1339,9458,4769,4689,3715,1890,1825
-Pre-laying vs. Laying,4247,1951,2296,2683,1795,888,5666,2654,3012
-Laying vs. post-laying,2803,978,1105,9456,4077,5379,2851,1264,1587
-Post-laying vs. Emerging,619,322,297,3536,2135,1401,619,322,297
-Post-laying vs. Non-laying,5,3,2,2,2,0,4,1,3
-Laying vs Non-laying,2203,1903,1110,13065,5738,7327,2203,1093,1110
-Emerging vs Phoretic,571,219,352,1492,889,603,571,219,352
-Emerging vs Young,1870,1011,859,8947,4465,4482,1870,1011,859
+Stages,M_DE,M_up-regulated,M_down-regulated,V_DE,V_up-regulated,V_down-regulated,V2_DE,V2_up-regulated,V2_down-regulated,V_gene_DE,V_gene_up-regulated,V_gene_down-regulated
+males vs young,5397,1596,3801,19220,8328,10892,8069,2641,5428,5759,2692,3067
+Young vs Phoretic,2852,1570,1282,12769,6846,5923,3374,1763,1611,4796,2463,2333
+Phoretics vs caged,1,0,1,0,0,0,23,13,10,51,27,24
+Phoretic vs arresting,68,19,49,3514,1288,2226,100,36,64,35,11,24
+Arrest vs pre-laying,1039,447,592,9458,4769,4689,2020,962,1058,3215,1647,1568
+Pre-laying vs. Laying,432,288,144,2683,1795,888,760,502,258,1473,799,674
+Laying vs. post-laying,2083,978,1105,9456,4077,5379,2851,1264,1587,3757,1741,2016
+Post-laying vs. Emerging,619,322,297,3536,2135,1401,700,292,408,1405,752,653
+Post-laying vs. Non-laying,5,3,2,2,2,0,4,1,3,2,2,0
+Laying vs Non-laying,2203,1093,1110,13065,5738,7327,3433,1529,1904,4602,2038,2564
+Emerging vs Phoretic,571,219,352,1492,889,603,600,352,248,866,448,418
+Emerging vs Young,1870,1011,859,8947,4465,4482,2505,1383,1122,4070,2135,1935
diff --git a/DE_varroa_mite.Rmd b/DE_varroa_mite.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "Varroa"
+title: "Varroa re-mapped"
 author: "Lazzat Aibekova"
 date: "6/04/2019"
 output: html_document
@@ -156,7 +156,7 @@ up_down_regulated
 ### Аrresting vs. pre-laying
 
 ```{r}
-so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "prelaying")), extra_bootstrap_summary = TRUE)
+so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("arresting", "prelaying")), extra_bootstrap_summary = TRUE)
 so <- sleuth_fit(so, ~condition, 'full')
 so <- sleuth_fit(so, ~1, 'reduced')
 so <- sleuth_lrt(so, 'reduced', 'full')
@@ -188,7 +188,7 @@ up_down_regulated
 ### Pre-laying vs. Laying
 
 ```{r}
-so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("phoretic", "laying")), extra_bootstrap_summary = TRUE)
+so <- sleuth_prep(dplyr::filter(samples, shortName %in% c("prelaying", "laying")), extra_bootstrap_summary = TRUE)
 so <- sleuth_fit(so, ~condition, 'full')
 so <- sleuth_fit(so, ~1, 'reduced')
 so <- sleuth_lrt(so, 'reduced', 'full')
@@ -203,8 +203,8 @@ models(so)
 ```
 Number of Differentially expressed genes (TRUE):
 ```{r}
-so = sleuth_wt(so, 'conditionphoretic')
-results_table = sleuth_results(so, 'conditionphoretic')
+so = sleuth_wt(so, 'conditionprelaying')
+results_table = sleuth_results(so, 'conditionprelaying')
 Number_DE_genes = table(results_table$qval <= 0.05)
 Number_DE_genes
 ```

diff --git a/Plots.Rmd b/Plots.Rmd
@@ -7,33 +7,54 @@ data = read.csv("/Users/lazzataibekova/Dropbox (OIST)/varroa microbiome/DE_varro
 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)
+```
diff --git a/Plots.nb.html b/Plots.nb.html