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24_GO_terms.R
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24_GO_terms.R
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########### 24 GO terms ##############
# GO_terms <- read.table("GO_terms", head = F)
library(gridExtra)
library(grid)
library(ggplot2)
library(lattice)
library(reshape2)
setwd("/Users/gaiaandreoletti/Documents/Phyton_Score/output_7Feb2019")
################################
# GO0045823_FPKM_Fisher__TACvehicle_discordance_score_genes #######
#############################
## Diff express ex matrix ####
## TAC veh / SHAM & ## TAC veh / TAC jq1 ### ###
DEgenes_TACvehvsTACjq1 = read.table('FPKM/GO0045823.txt_FPKM_Fisher__DEgenes_TACvehvsTACjq1.txt.txt')
DEgenes_TACvehvsSHAM = read.table('FPKM/GO0045823.txt_FPKM_Fisher__DEgenes_TACvehvsSHAM.txt.txt')
data_DEgenes_TACvehvsSHAM <-
data.frame(P_A=c(DEgenes_TACvehvsSHAM$V1),
NP_A=c(DEgenes_TACvehvsSHAM$V2),
P_B=c(DEgenes_TACvehvsSHAM$V3),
NP_B=c(DEgenes_TACvehvsSHAM$V4))
DEgenes_TACvehvsTACjq1 <-
data.frame(P_A=c(DEgenes_TACvehvsTACjq1$V1),
NP_A=c(DEgenes_TACvehvsTACjq1$V2),
P_B=c(DEgenes_TACvehvsTACjq1$V3),
NP_B=c(DEgenes_TACvehvsTACjq1$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
pvlue_data_DEgenes_TACvehvsSHAM = apply(data_DEgenes_TACvehvsSHAM, 1, rowFisher)
pvlue_DEgenes_TACvehvsTACjq1 = apply(DEgenes_TACvehvsTACjq1, 1, rowFisher)
triage = read.table('FPKM/GO0045823.txt_FPKM_Fisher_TACvehicle_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0045823.txt_FPKM_Fisher_TAC_vehicle_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACvehiclepvlue_triage = apply(data_triage, 1, rowFisher)
TACvehiclepvlue_exp = apply(data_exp, 1, rowFisher)
# #pvlue_triage = append(pvlue_triage, 1.000000e+00)
# #pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( TACvehiclepvlue_triage,TACvehiclepvlue_exp, pvlue_data_DEgenes_TACvehvsSHAM,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression","DEgenes_TACvehvsSHAM","DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0045823_FPKM_TACveh <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0045823 positive regulation of heart contraction",
subtitle = "TAC veh data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 12) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0045823_FPKM_TACveh + theme(legend.position="bottom")
################################
# GO0045823_FPKM_Fisher__TACjq1icle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0045823.txt_FPKM_Fisher_TACj_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0045823.txt_FPKM_Fisher_TACjq1_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACjq1pvlue_triage = apply(data_triage, 1, rowFisher)
TACjq1pvlue_exp = apply(data_exp, 1, rowFisher)
##pvlue_triage = append(pvlue_triage, 1.000000e+00)
##pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( TACjq1pvlue_triage,TACjq1pvlue_exp,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0045823_FPKM_TACjq1 <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0045823 positive regulation of heart contraction",
subtitle = "TAC jq1 data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 12) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0045823_FPKM_TACjq1 + theme(legend.position="bottom")
################################
# GO0045823_FPKM_Fisher__SHAMicle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0045823.txt_FPKM_Fisher_Sham_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0045823.txt_FPKM_Fisher_Sham_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
Sham_pvlue_triage = apply(data_triage, 1, rowFisher)
Sham_pvlue_exp = apply(data_exp, 1, rowFisher)
##pvlue_triage = append(pvlue_triage, 1.000000e+00)
##pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( Sham_pvlue_triage,Sham_pvlue_exp,pvlue_data_DEgenes_TACvehvsSHAM)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsSHAM")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0045823_FPKM_SHAM <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0045823 positive regulation of heart contraction",
subtitle = "SHAM data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 12) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0045823_FPKM_SHAM + theme(legend.position="bottom")
#pdf("GO0045823_positive_regulation_of_heart_contraction.#pdf")
#grid.arrange(GO0045823_FPKM_TACveh,GO0045823_FPKM_TACjq1,GO0045823_FPKM_SHAM, ncol=1)
dev.off()
merged.data = cbind(Sham_pvlue_triage,TACvehiclepvlue_triage,TACjq1pvlue_triage)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("SHAM_triage","TAC_triage", "TACjq1_triage")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0045823_FPKM_all <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0045823 positive regulation of heart contraction",
subtitle = "SHAM, TAC veh, TAC JQ1 traige data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 12) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
################################
# GO0008016_FPKM_Fisher__TACvehicle_discordance_score_genes #######
#############################
## Diff express ex matrix ####
## TAC veh / SHAM & ## TAC veh / TAC jq1 ### ###
DEgenes_TACvehvsTACjq1 = read.table('FPKM/GO0008016.txt_FPKM_Fisher__DEgenes_TACvehvsTACjq1.txt.txt')
DEgenes_TACvehvsSHAM = read.table('FPKM/GO0008016.txt_FPKM_Fisher__DEgenes_TACvehvsSHAM.txt.txt')
data_DEgenes_TACvehvsSHAM <-
data.frame(P_A=c(DEgenes_TACvehvsSHAM$V1),
NP_A=c(DEgenes_TACvehvsSHAM$V2),
P_B=c(DEgenes_TACvehvsSHAM$V3),
NP_B=c(DEgenes_TACvehvsSHAM$V4))
DEgenes_TACvehvsTACjq1 <-
data.frame(P_A=c(DEgenes_TACvehvsTACjq1$V1),
NP_A=c(DEgenes_TACvehvsTACjq1$V2),
P_B=c(DEgenes_TACvehvsTACjq1$V3),
NP_B=c(DEgenes_TACvehvsTACjq1$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
pvlue_data_DEgenes_TACvehvsSHAM = apply(data_DEgenes_TACvehvsSHAM, 1, rowFisher)
pvlue_DEgenes_TACvehvsTACjq1 = apply(DEgenes_TACvehvsTACjq1, 1, rowFisher)
triage = read.table('FPKM/GO0008016_FPKM_Fisher__TACvehicle_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0008016.txt_FPKM_Fisher_TAC_vehicle_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACvehiclepvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
# #pvlue_triage = append(pvlue_triage, 1.000000e+00)
# #pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp, pvlue_data_DEgenes_TACvehvsSHAM,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression","DEgenes_TACvehvsSHAM","DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0008016_FPKM_TACveh <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0008016 regulation of heart contraction",
subtitle = "TAC veh data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 40) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0008016_FPKM_TACveh + theme(legend.position="bottom")
################################
# GO0008016_FPKM_Fisher__TACjq1icle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0008016.txt_FPKM_Fisher_TACj_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0008016.txt_FPKM_Fisher_TACjq1_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACjq1pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)
#pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0008016_FPKM_TACjq1 <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0008016 regulation of heart contraction",
subtitle = "TAC jq1 data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 40) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0008016_FPKM_TACjq1 + theme(legend.position="bottom")
################################
# GO0008016_FPKM_Fisher__SHAMicle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0008016.txt_FPKM_Fisher_Sham_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0008016.txt_FPKM_Fisher_Sham_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
Sham_pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)
#pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp,pvlue_data_DEgenes_TACvehvsSHAM)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsSHAM")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0008016_FPKM_SHAM <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0008016 regulation of heart contraction",
subtitle = "SHAM data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 40) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0008016_FPKM_SHAM + theme(legend.position="bottom")
#pdf("GO0008016_regulation_ofHeartContraction.#pdf")
#grid.arrange(GO0008016_FPKM_TACveh,GO0008016_FPKM_TACjq1,GO0008016_FPKM_SHAM, ncol=1)
dev.off()
merged.data = cbind(Sham_pvlue_triage,TACvehiclepvlue_triage,TACjq1pvlue_triage)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("SHAM_triage","TAC_triage", "TACjq1_triage")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0008016_FPKM_all <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0008016 regulation of heart contraction",
subtitle = "SHAM, TAC veh, TAC JQ1 traige data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
################################
# GO0086091_FPKM_Fisher__TACvehicle_discordance_score_genes #######
#############################
## Diff express ex matrix ####
## TAC veh / SHAM & ## TAC veh / TAC jq1 ### ###
DEgenes_TACvehvsTACjq1 = read.table('FPKM/GO0086091.txt_FPKM_Fisher__DEgenes_TACvehvsTACjq1.txt.txt')
DEgenes_TACvehvsSHAM = read.table('FPKM/GO0086091.txt_FPKM_Fisher__DEgenes_TACvehvsSHAM.txt.txt')
data_DEgenes_TACvehvsSHAM <-
data.frame(P_A=c(DEgenes_TACvehvsSHAM$V1),
NP_A=c(DEgenes_TACvehvsSHAM$V2),
P_B=c(DEgenes_TACvehvsSHAM$V3),
NP_B=c(DEgenes_TACvehvsSHAM$V4))
DEgenes_TACvehvsTACjq1 <-
data.frame(P_A=c(DEgenes_TACvehvsTACjq1$V1),
NP_A=c(DEgenes_TACvehvsTACjq1$V2),
P_B=c(DEgenes_TACvehvsTACjq1$V3),
NP_B=c(DEgenes_TACvehvsTACjq1$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
pvlue_data_DEgenes_TACvehvsSHAM = apply(data_DEgenes_TACvehvsSHAM, 1, rowFisher)
pvlue_DEgenes_TACvehvsTACjq1 = apply(DEgenes_TACvehvsTACjq1, 1, rowFisher)
triage = read.table('FPKM/GO0086091.txt_FPKM_Fisher_TACvehicle_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0086091.txt_FPKM_Fisher_TAC_vehicle_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACvehiclepvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
# #pvlue_triage = append(pvlue_triage, 1.000000e+00)
# #pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp, pvlue_data_DEgenes_TACvehvsSHAM,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression","DEgenes_TACvehvsSHAM","DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0086091_FPKM_TACveh <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0086091 regulation of heart rate by cardiac conduction",
subtitle = "TAC veh data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 12) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0086091_FPKM_TACveh + theme(legend.position="bottom")
################################
# GO0086091_FPKM_Fisher__TACjq1icle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0086091.txt_FPKM_Fisher_TACj_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0086091.txt_FPKM_Fisher_TACjq1_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACjq1pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)
#pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0086091_FPKM_TACjq1 <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0086091 regulation of heart rate by cardiac conduction",
subtitle = "TAC jq1 data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 12) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0086091_FPKM_TACjq1 + theme(legend.position="bottom")
## QUI ##
################################
# GO0086091_FPKM_Fisher__SHAMicle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0086091.txt_FPKM_Fisher_Sham_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0086091.txt_FPKM_Fisher_Sham_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
Sham_pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)
#pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp,pvlue_data_DEgenes_TACvehvsSHAM)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsSHAM")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0086091_FPKM_SHAM <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0086091 regulation of heart rate by cardiac conduction",
subtitle = "SHAM data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 12) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0086091_FPKM_SHAM + theme(legend.position="bottom")
#pdf("GO0086091_regulationOf_heartRateByCardiacConduction.#pdf")
#grid.arrange(GO0086091_FPKM_TACveh,GO0086091_FPKM_TACjq1,GO0086091_FPKM_SHAM, ncol=1)
dev.off()
merged.data = cbind(Sham_pvlue_triage,TACvehiclepvlue_triage,TACjq1pvlue_triage)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("SHAM_triage","TAC_triage", "TACjq1_triage")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0086091_FPKM_all <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0086091 regulation of heart rate by cardiac conduction",
subtitle = "SHAM, TAC veh, TAC JQ1 traige data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
################################
# GO0060047_FPKM_Fisher__TACvehicle_discordance_score_genes #######
#############################
## Diff express ex matrix ####
## TAC veh / SHAM & ## TAC veh / TAC jq1 ### ###
DEgenes_TACvehvsTACjq1 = read.table('FPKM/GO0060047.txt_FPKM_Fisher__DEgenes_TACvehvsTACjq1.txt.txt')
DEgenes_TACvehvsSHAM = read.table('FPKM/GO0060047.txt_FPKM_Fisher__DEgenes_TACvehvsSHAM.txt.txt')
data_DEgenes_TACvehvsSHAM <-
data.frame(P_A=c(DEgenes_TACvehvsSHAM$V1),
NP_A=c(DEgenes_TACvehvsSHAM$V2),
P_B=c(DEgenes_TACvehvsSHAM$V3),
NP_B=c(DEgenes_TACvehvsSHAM$V4))
DEgenes_TACvehvsTACjq1 <-
data.frame(P_A=c(DEgenes_TACvehvsTACjq1$V1),
NP_A=c(DEgenes_TACvehvsTACjq1$V2),
P_B=c(DEgenes_TACvehvsTACjq1$V3),
NP_B=c(DEgenes_TACvehvsTACjq1$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
pvlue_data_DEgenes_TACvehvsSHAM = apply(data_DEgenes_TACvehvsSHAM, 1, rowFisher)
pvlue_DEgenes_TACvehvsTACjq1 = apply(DEgenes_TACvehvsTACjq1, 1, rowFisher)
triage = read.table('FPKM/GO0060047.txt_FPKM_Fisher_TACvehicle_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0060047.txt_FPKM_Fisher_TAC_vehicle_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACvehiclepvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
# #pvlue_triage = append(pvlue_triage, 1.000000e+00)
# #pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp, pvlue_data_DEgenes_TACvehvsSHAM,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression","DEgenes_TACvehvsSHAM","DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0060047_FPKM_TACveh <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0060047 heart contraction",
subtitle = "TAC veh data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 5) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0060047_FPKM_TACveh + theme(legend.position="bottom")
################################
# GO0060047_FPKM_Fisher__TACjq1icle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0060047.txt_FPKM_Fisher_TACj_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0060047.txt_FPKM_Fisher_TACjq1_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACjq1pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)
#pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0060047_FPKM_TACjq1 <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0060047 heart contraction",
subtitle = "TAC jq1 data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 5) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0060047_FPKM_TACjq1 + theme(legend.position="bottom")
################################
# GO0060047_FPKM_Fisher__SHAMicle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0060047.txt_FPKM_Fisher_Sham_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0060047.txt_FPKM_Fisher_Sham_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
Sham_pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)
#pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp,pvlue_data_DEgenes_TACvehvsSHAM)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsSHAM")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0060047_FPKM_SHAM <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0060047 heart contraction",
subtitle = "SHAM data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 5) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0060047_FPKM_SHAM + theme(legend.position="bottom")
#pdf("GO0060047_heartContraction.#pdf")
#grid.arrange(GO0060047_FPKM_TACveh,GO0060047_FPKM_TACjq1,GO0060047_FPKM_SHAM, ncol=1)
dev.off()
merged.data = cbind(Sham_pvlue_triage,TACvehiclepvlue_triage,TACjq1pvlue_triage)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("SHAM_triage","TAC_triage", "TACjq1_triage")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0060047_FPKM_all <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0060047 heart contraction",
subtitle = "SHAM, TAC veh, TAC JQ1 traige data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
################################
# GO0002448_FPKM_Fisher__TACvehicle_discordance_score_genes #######
#############################
## Diff express ex matrix ####
## TAC veh / SHAM & ## TAC veh / TAC jq1 ### ###
DEgenes_TACvehvsTACjq1 = read.table('FPKM/GO0002448.txt_FPKM_Fisher__DEgenes_TACvehvsTACjq1.txt.txt')
DEgenes_TACvehvsSHAM = read.table('FPKM/GO0002448.txt_FPKM_Fisher__DEgenes_TACvehvsSHAM.txt.txt')
data_DEgenes_TACvehvsSHAM <-
data.frame(P_A=c(DEgenes_TACvehvsSHAM$V1),
NP_A=c(DEgenes_TACvehvsSHAM$V2),
P_B=c(DEgenes_TACvehvsSHAM$V3),
NP_B=c(DEgenes_TACvehvsSHAM$V4))
DEgenes_TACvehvsTACjq1 <-
data.frame(P_A=c(DEgenes_TACvehvsTACjq1$V1),
NP_A=c(DEgenes_TACvehvsTACjq1$V2),
P_B=c(DEgenes_TACvehvsTACjq1$V3),
NP_B=c(DEgenes_TACvehvsTACjq1$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
pvlue_data_DEgenes_TACvehvsSHAM = apply(data_DEgenes_TACvehvsSHAM, 1, rowFisher)
pvlue_DEgenes_TACvehvsTACjq1 = apply(DEgenes_TACvehvsTACjq1, 1, rowFisher)
triage = read.table('FPKM/GO0002448.txt_FPKM_Fisher_TACvehicle_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0002448.txt_FPKM_Fisher_TAC_vehicle_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACvehiclepvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
# #pvlue_triage = append(pvlue_triage, 1.000000e+00)
# #pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp, pvlue_data_DEgenes_TACvehvsSHAM,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression","DEgenes_TACvehvsSHAM","DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0002448_FPKM_TACveh <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0002448 mast cell mediated immunity ",
subtitle = "TAC veh data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 4) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0002448_FPKM_TACveh + theme(legend.position="bottom")
################################
# GO0002448_FPKM_Fisher__TACjq1icle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0002448.txt_FPKM_Fisher_TACj_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0002448.txt_FPKM_Fisher_TACjq1_expression_value_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
TACjq1pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)
#pvlue_exp = append(pvlue_exp, 1.000000e+00)
merged.data = cbind( pvlue_triage,pvlue_exp,pvlue_DEgenes_TACvehvsTACjq1)
merged.data = as.data.frame(merged.data)
colnames(merged.data) <- c("Triage","Expression", "DEgenes_TACvehvsTACjq1")
merged.data$rank = seq(1:nrow(merged.data))
dim(merged.data)
head(merged.data,10)
merged.data = merged.data[-1,]
f_melt = melt(merged.data, id = "rank")
#View(f_melt)
GO0002448_FPKM_TACjq1 <- ggplot(f_melt, aes(x = rank, y = -log10(value), colour = variable)) +
geom_line(aes(color=variable)) +
#geom_point(aes(color=variable), size=1, shape = 15) +
xlim(0, 100) +
labs(title = "GO0002448 mast cell mediated immunity ",
subtitle = "TAC jq1 data",
x = "Rank",
y = "- log10 pvalue") +
theme_bw() + ylim(NA, 4) + theme (panel.grid.major = element_blank(),
panel.grid.minor = element_blank()) +theme(aspect.ratio = 1)
GO0002448_FPKM_TACjq1 + theme(legend.position="bottom")
################################
# GO0002448_FPKM_Fisher__SHAMicle_discordance_score_genes
#############################
triage = read.table('FPKM/GO0002448.txt_FPKM_Fisher_Sham_discordance_score_genes.txt', header = F)
exp = read.table('FPKM/GO0002448.txt_FPKM_Fisher_Sham_discordance_score_genes.txt', header = F)
data_triage <-
data.frame(P_A=c(triage$V1),
NP_A=c(triage$V2),
P_B=c(triage$V3),
NP_B=c(triage$V4))
data_exp <-
data.frame(P_A=c(exp$V1),
NP_A=c(exp$V2),
P_B=c(exp$V3),
NP_B=c(exp$V4))
rowFisher <- function(x, ...) {
return(fisher.test(matrix(x, nrow = 2, ...), alternative = "greater")$p.value)
}
Sham_pvlue_triage = apply(data_triage, 1, rowFisher)
pvlue_exp = apply(data_exp, 1, rowFisher)
#pvlue_triage = append(pvlue_triage, 1.000000e+00)