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16A_boxplots_a_vs_z_after_removing_SBG.R
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#Boxplots A vs Z, after removing SBG
#Clear all states
rm(list=ls(all=TRUE))
dev.off()
############### Paths and folders
### Folder containind expression data before removing SBG
folder_1 <- "/crex/proj/uppstore2017185/b2014034_nobackup/Luis/3_DosageCompensation_LS/03_Normalized_libs"
### Folder containind expression data after removing SBG
folder_2 <-"/crex/proj/uppstore2017185/b2014034_nobackup/Luis/3_DosageCompensation_LS/12_Filter_sex_biased_genes"
############## Load data
### First dataset
setwd(folder_1)
# Before removing SBG; genes with zero counts removed individually for each sex
instar_V_f <- read.delim("instar_V-assigned_A_or_Z_female-filtered.txt", header = TRUE)
instar_V_m <- read.delim("instar_V-assigned_A_or_Z_male-filtered.txt", header = TRUE)
pupa_f <- read.delim("pupa-assigned_A_or_Z_female-filtered.txt", header = TRUE)
pupa_m <- read.delim("pupa-assigned_A_or_Z_male-filtered.txt", header = TRUE)
adult_f <- read.delim("adult-assigned_A_or_Z_female-filtered.txt", header = TRUE)
adult_m <- read.delim("adult-assigned_A_or_Z_male-filtered.txt", header = TRUE)
### Second dataset
setwd(folder_2)
####### After removing SBG; genes with zero counts removed individually for each sex
instar_V_f_nonbiased <- read.delim("nonbiased_genes-instar_V-assigned_A_or_Z_female-filtered.txt", header = TRUE)
instar_V_m_nonbiased <- read.delim("nonbiased_genes-instar_V-assigned_A_or_Z_male-filtered.txt", header = TRUE)
pupa_f_nonbiased <- read.delim("nonbiased_genes-pupa-assigned_A_or_Z_female-filtered.txt", header = TRUE)
pupa_m_nonbiased <- read.delim("nonbiased_genes-pupa-assigned_A_or_Z_male-filtered.txt", header = TRUE)
adult_f_nonbiased <- read.delim("nonbiased_genes-adult-assigned_A_or_Z_female-filtered.txt", header = TRUE)
adult_m_nonbiased <- read.delim("nonbiased_genes-adult-assigned_A_or_Z_male-filtered.txt", header = TRUE)
##################################### PROCESS DATA
############### Dataset I
instar_V_female <- instar_V_f[c(4,6)]
instar_V_female$group <- rep("1_instar_V_female", nrow(instar_V_female))
instar_V_female$group <- paste(instar_V_female$group, instar_V_female$chromosome)
instar_V_female <- instar_V_female[c(1,3)]
names(instar_V_female)[1] <-"FPKM"
pupa_female <- pupa_f[c(4,6)]
pupa_female$group <- rep("3_pupa_female", nrow(pupa_female))
pupa_female$group <- paste(pupa_female$group, pupa_female$chromosome)
pupa_female <- pupa_female[c(1,3)]
names(pupa_female)[1] <-"FPKM"
adult_female <- adult_f[c(4,6)]
adult_female$group <- rep("5_adult_female", nrow(adult_female))
adult_female$group <- paste(adult_female$group, adult_female$chromosome)
adult_female <- adult_female[c(1,3)]
names(adult_female)[1] <-"FPKM"
instar_V_male <- instar_V_m[c(5,6)]
instar_V_male$group <- rep("2_instar_V_male", nrow(instar_V_male))
instar_V_male$group <- paste(instar_V_male$group, instar_V_male$chromosome)
instar_V_male <- instar_V_male[c(1,3)]
names(instar_V_male)[1] <-"FPKM"
pupa_male <- pupa_m[c(5,6)]
pupa_male$group <- rep("4_pupa_male", nrow(pupa_male))
pupa_male$group <- paste(pupa_male$group, pupa_male$chromosome)
pupa_male <- pupa_male[c(1,3)]
names(pupa_male)[1] <-"FPKM"
adult_male <- adult_m[c(5,6)]
adult_male$group <- rep("6_adult_male", nrow(adult_male))
adult_male$group <- paste(adult_male$group, adult_male$chromosome)
adult_male <- adult_male[c(1,3)]
names(adult_male)[1] <-"FPKM"
all_samples <- rbind(instar_V_female, instar_V_male, pupa_female, pupa_male, adult_female, adult_male)
############### Dataset II
instar_V_female_nonbiased <- instar_V_f_nonbiased[c(4,6)]
instar_V_female_nonbiased$group <- rep("1_instar_V_female_nonbiased", nrow(instar_V_female_nonbiased))
instar_V_female_nonbiased$group <- paste(instar_V_female_nonbiased$group, instar_V_female_nonbiased$chromosome)
instar_V_female_nonbiased <- instar_V_female_nonbiased[c(1,3)]
names(instar_V_female_nonbiased)[1] <-"FPKM"
pupa_female_nonbiased <- pupa_f_nonbiased[c(4,6)]
pupa_female_nonbiased$group <- rep("3_pupa_female_nonbiased", nrow(pupa_female_nonbiased))
pupa_female_nonbiased$group <- paste(pupa_female_nonbiased$group, pupa_female_nonbiased$chromosome)
pupa_female_nonbiased <- pupa_female_nonbiased[c(1,3)]
names(pupa_female_nonbiased)[1] <-"FPKM"
adult_female_nonbiased <- adult_f_nonbiased[c(4,6)]
adult_female_nonbiased$group <- rep("5_adult_female_nonbiased", nrow(adult_female_nonbiased))
adult_female_nonbiased$group <- paste(adult_female_nonbiased$group, adult_female_nonbiased$chromosome)
adult_female_nonbiased <- adult_female_nonbiased[c(1,3)]
names(adult_female_nonbiased)[1] <-"FPKM"
instar_V_male_nonbiased <- instar_V_m_nonbiased[c(5,6)]
instar_V_male_nonbiased$group <- rep("2_instar_V_male_nonbiased", nrow(instar_V_male_nonbiased))
instar_V_male_nonbiased$group <- paste(instar_V_male_nonbiased$group, instar_V_male_nonbiased$chromosome)
instar_V_male_nonbiased <- instar_V_male_nonbiased[c(1,3)]
names(instar_V_male_nonbiased)[1] <-"FPKM"
pupa_male_nonbiased <- pupa_m_nonbiased[c(5,6)]
pupa_male_nonbiased$group <- rep("4_pupa_male_nonbiased", nrow(pupa_male_nonbiased))
pupa_male_nonbiased$group <- paste(pupa_male_nonbiased$group, pupa_male_nonbiased$chromosome)
pupa_male_nonbiased <- pupa_male_nonbiased[c(1,3)]
names(pupa_male_nonbiased)[1] <-"FPKM"
adult_male_nonbiased <- adult_m_nonbiased[c(5,6)]
adult_male_nonbiased$group <- rep("6_adult_male_nonbiased", nrow(adult_male_nonbiased))
adult_male_nonbiased$group <- paste(adult_male_nonbiased$group, adult_male_nonbiased$chromosome)
adult_male_nonbiased <- adult_male_nonbiased[c(1,3)]
names(adult_male_nonbiased)[1] <-"FPKM"
nonbiased <- rbind(instar_V_female_nonbiased, instar_V_male_nonbiased, pupa_female_nonbiased, pupa_male_nonbiased, adult_female_nonbiased, adult_male_nonbiased)
##############################################################################
### Boxplot
boxplot(log2(all_samples$FPKM)~all_samples$group, ylim = c(-6, 18),
col = c("grey90", "grey90"), notch = TRUE,
at = c(1,2, 4,5, 8,9, 11,12, 15,16, 18,19),
outline = FALSE, boxwex = 0.7, xaxt = "n", frame.plot = FALSE, border="grey65",
boxlty = 2)
axis(2, labels = "log2 FPKM(>0)", cex.axis = 1.2, at = 4, line = 1.5, tck = 0)
boxplot(log2(nonbiased$FPKM)~nonbiased$group, ylim = c(-8, 14), add = TRUE,
col = c("lightgrey", "darkorange"), notch = FALSE,
at = c(1.2,2.2, 4.2,5.2, 8.2,9.2, 11.2,12.2, 15.2,16.2, 18.2,19.2),
outline = FALSE, boxwex = 0.7, xaxt = "n", frame.plot = FALSE)
text(1.5, -6.5, "\\VE", vfont=c("sans serif","plain"), cex =1.9)
text(4.5, -6.5, "\\MA", vfont=c("sans serif","plain"), cex =1.9)
text(8.5, -6.5, "\\VE", vfont=c("sans serif","plain"), cex =1.9)
text(11.5, -6.5, "\\MA", vfont=c("sans serif","plain"), cex =1.9)
text(15.5, -6.5, "\\VE", vfont=c("sans serif","plain"), cex =1.9)
text(18.5, -6.5, "\\MA", vfont=c("sans serif","plain"), cex =1.9)
axis(1, labels = c("Larva", "Pupa", "Adult"), lwd = 0, cex.axis = 1.5,
at = c(3, 10, 17), line = 1)
legend(16.5, 18, legend = c("Autosomes","Z"), cex = 1,
fill = c("lightgrey", "darkorange"), bty = "n")
#legend(0.5, 19, legend = c("Autosomes","Z"), cex = 1,
# fill = c("lightgrey", "darkorange"), bty = "n")
segments(6.5, -5.5, 6.5, 15, lty = 3, lwd = 1)
segments(13.5, -5.5, 13.5, 15, lty = 3, lwd = 1)
segments(1, -5.5, 19, -5.5, lty = 1, lwd = 1)