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volcano_and_counts.R
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library(tidyverse)
library(readr)
####################################################################################
#Kidney
Xie_difexpr_kidney_results_dic <- read_csv("Xie_kidney_swish.csv")
#############################################
library(ggplot2)
library(ggthemes)
Xie_kidney_results_dic_mod<- Xie_difexpr_kidney_results_dic
# add a column of NAs
Xie_kidney_results_dic_mod$diffexpressed <- "NO"
# if log2Foldchange > 0.5 and pvalue < 0.05, set as "UP"
Xie_kidney_results_dic_mod$diffexpressed[Xie_kidney_results_dic_mod$log2FC > 0.5 &
Xie_kidney_results_dic_mod$pvalue < 0.05] <- "UP"
# if log2Foldchange < -0.5 and pvalue < 0.05, set as "DOWN"
Xie_kidney_results_dic_mod$diffexpressed[Xie_kidney_results_dic_mod$log2FC < -0.5 &
Xie_kidney_results_dic_mod$pvalue < 0.05] <- "DOWN"
Xie_kidney_results_dic_mod %>%
filter(abs(log2FC)> 0.01) %>%
ggplot(aes(x= log2FC, y= -log10(pvalue), col = diffexpressed))+
geom_point()+
scale_color_manual(values= c("blue", "grey", "red"))+
geom_vline(xintercept=c(-0.5, 0.5), col="red") +
geom_hline(yintercept=-log10(0.05), col="red")
#####################################
#barplot
xie_kidney_DTEs_dic <- Xie_kidney_results_dic_mod %>% filter(pvalue <0.05 & abs(log2FoldChange) > 0.5)
#DTEs_lncRNA <- xie_kidney_DTEs_dic %>% filter(transcript_type == "lncRNA")
xie_kidney_DTEs_dic %>%
filter(transcript_type %in% c("protein_coding", "retained_intron", "nonsense_mediated_decay",
"processed_transcript", "lncRNA")) %>%
ggplot(aes(x=transcript_type))+
geom_bar(aes(fill = diffexpressed))+
scale_fill_manual(values= c("blue", "red3"))
#theme(axis.text.x = element_text(angle = 45))
########################################################
#####################
library(tidyverse)
####################################################################################
#lung
Xie_difexpr_lung_results_dic <- read_csv("Xie_lung_swish.csv")
#############################################
library(ggplot2)
library(tidyverse)
library(ggthemes)
Xie_lung_results_dic_mod<- Xie_difexpr_lung_results_dic
# add a column of NAs
Xie_lung_results_dic_mod$diffexpressed <- "NO"
# if log2Foldchange > 0.6 and pvalue < 0.05, set as "UP"
Xie_lung_results_dic_mod$diffexpressed[Xie_lung_results_dic_mod$log2FC > 0.5 &
Xie_lung_results_dic_mod$pvalue < 0.05] <- "UP"
# if log2Foldchange < -0.6 and pvalue < 0.05, set as "DOWN"
Xie_lung_results_dic_mod$diffexpressed[Xie_lung_results_dic_mod$log2FC < -0.5 &
Xie_lung_results_dic_mod$pvalue < 0.05] <- "DOWN"
Xie_lung_results_dic_mod %>%
#filter(-log10(pvalue))%>%
filter(abs(log2FC)> 0.01) %>%
ggplot(aes(x= log2FC, y= -log10(pvalue), col = diffexpressed))+
geom_point()+
scale_color_manual(values= c("blue", "grey", "red"))+
geom_vline(xintercept=c(-0.5, 0.5), col="red") +
geom_hline(yintercept=-log10(0.05), col="red")
#####################################
#barplot
xie_lung_DTEs_dic <- Xie_lung_results_dic_mod %>% filter(pvalue <0.05 & abs(log2FoldChange) > 0.5)
#DTEs_lncRNA <- xie_kidney_DTEs_dic %>% filter(transcript_type == "lncRNA")
xie_lung_DTEs_dic %>%
filter(transcript_type %in% c("protein_coding", "retained_intron", "nonsense_mediated_decay",
"processed_transcript", "lncRNA")) %>%
ggplot(aes(x=transcript_type))+
geom_bar(aes(fill = diffexpressed))+
scale_fill_manual(values= c("blue", "red3"))
#theme(axis.text.x = element_text(angle = 45))