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NCC_RNAseq_45X/NCCs_IF_v01_pass.R

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#PAX7&SOX10 CHIR
require(rstatix)
require(ggpubr)
require(ggprism)
IF_percent_PAX7SOX10_CHIR<-read.csv("MS4_IF_percent_PAX7SOX10.csv", header = T)
PAX7SOX10_fem <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Female") %>%
filter(Cell_Line != "C6XX")
PAX7SOX10_male1 <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Male1")
PAX7SOX10_male1$Cell_Line <- factor(PAX7SOX10_male1$Cell_Line, levels = c("XY", "XO"))
PAX7SOX10_male2 <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Male2")
PAX7SOX10_male2$Cell_Line <- factor(PAX7SOX10_male2$Cell_Line, levels = c("C21XY", "C69XY", "C70XY", "C85XY", "C7XO", "C15XO"))
bp_fem <- ggplot(PAX7SOX10_fem, aes(Cell_Line, perc_PAX7SOX10, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype), show.legend = FALSE) + scale_color_manual(values = c("violet", "purple")) +
theme(text=element_text(size=5)) +
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent PAX7+/SOX10+")
bp_fem
ggsave("PAX7SOX10_CHIR_Female.pdf", width = 2.5, height = 1.6)
bp_male1 <- ggplot(PAX7SOX10_male1, aes(Cell_Line, perc_PAX7SOX10, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype), show.legend = FALSE) + scale_color_manual(values = c("deepskyblue", "blue")) +
theme(text=element_text(size=5)) +
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent PAX7+/SOX10+")
bp_male1
ggsave("PAX7SOX10_CHIR_male1.pdf", width = 2.5, height = 1.6)
bp_male2 <- ggplot(PAX7SOX10_male2, aes(Cell_Line, perc_PAX7SOX10, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype), show.legend = FALSE) + scale_color_manual(values = c("springgreen", "darkgreen")) +
theme(text=element_text(size=5)) + #change font size of all text
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent PAX7+/SOX10+")
bp_male2
ggsave("PAX7SOX10_CHIR_male2.pdf", width = 2.5, height = 1.6)
XY_CHIR <- subset(IF_percent_PAX7SOX10_CHIR, IF_percent_PAX7SOX10_CHIR$Cell_Line=="XY")
XY_CHIR <- XY_CHIR$perc_PAX7SOX10
XO_CHIR <- subset(IF_percent_PAX7SOX10_CHIR, IF_percent_PAX7SOX10_CHIR$Cell_Line=="XO")
XO_CHIR <- XO_CHIR$perc_PAX7SOX10
wilcox.test(XO_CHIR, XY_CHIR)
#p=0.016
C7C15_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C7XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C15XO"),]
C7C15_CHIR <- C7C15_CHIR$perc_PAX7SOX10
C21C69C70C85 <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C21XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C69XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C70XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C85XY"),]
C21C69C70C85 <- C21C69C70C85$perc_PAX7SOX10
wilcox.test(C7C15_CHIR, C21C69C70C85)
#p=1e-05
fXOs_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C8XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C9XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C2XO"), "perc_PAX7SOX10"]
wilcox.test(fXOs_CHIR, C19C23_CHIR)
#p=0.3
wilcox.test(fXOs_CHIR, C21C69C70C85)
#p=0.00113
wilcox.test(fXOs_CHIR, XY_CHIR)
#p=0.00058
#PAX7
PAX7_fem <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Female") %>%
filter(Cell_Line != "C6XX")
PAX7_fem$Cell_Line <- factor(PAX7_fem$Cell_Line, levels = c( "C19XX", "C23XX", "C2XO", "C8XO", "C9XO"))
bp_fem_PAX7 <- ggplot(PAX7_fem, aes(Cell_Line, perc_PAX7, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype)) + scale_color_manual(values = c("violet", "purple")) +
theme(text=element_text(size=5)) +
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent PAX7+")
bp_fem_PAX7
ggsave("PAX7_CHIR_female.pdf", width = 2.5, height = 1.6)
PAX7_male1 <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Male1")
PAX7_male1$Cell_Line <- factor(PAX7_male1$Cell_Line, levels = c("XY", "XO"))
bp_male1_PAX7 <- ggplot(PAX7_male1, aes(Cell_Line, perc_PAX7, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype)) + scale_color_manual(values = c("deepskyblue", "blue")) +
theme(text=element_text(size=5)) +
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent PAX7+/SOX10+")
bp_male1_PAX7
ggsave("PAX7_CHIR_male1.pdf", width = 2.5, height = 1.6)
PAX7_male2 <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Male2")
PAX7_male2$Cell_Line <- factor(PAX7_male2$Cell_Line, levels = c("C21XY", "C69XY", "C70XY", "C85XY", "C7XO", "C15XO"))
bp_male2_PAX7 <- ggplot(PAX7_male2, aes(Cell_Line, perc_PAX7, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype)) + scale_color_manual(values = c("springgreen", "darkgreen")) +
theme(text=element_text(size=5)) + #change font size of all text
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent PAX7+")
bp_male2_PAX7
ggsave("PAX7_CHIR_male2.pdf", width = 2.5, height = 1.6)
All_Euploids <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C21XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C69XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C70XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C85XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C19XX" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C23XX"),"perc_PAX7"]
All_XOs <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C7XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C15XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C8XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C9XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C2XO"),"perc_PAX7"]
wilcox.test(All_XOs, All_Euploids)
#p=0.00004
XY_PAX7_CHIR <-IF_percent_PAX7SOX10_CHIR [which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="XY"), "perc_PAX7"]
XO_PAX7_CHIR <- IF_percent_PAX7SOX10_CHIR [which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="XO"), "perc_PAX7"]
wilcox.test(XY_PAX7_CHIR, XO_PAX7_CHIR)
#p=0.067
C21C69C70C85_PAX7_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C21XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C69XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C70XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C85XY"), "perc_PAX7"]
C7C15_PAX7_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C7XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C15XO"), "perc_PAX7"]
wilcox.test(C21C69C70C85_PAX7_CHIR, C7C15_PAX7_CHIR)
#p=0.07
All_Euploids_PAX7_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C21XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C69XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C70XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C85XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C19XX" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C23XX"), "perc_PAX7"]
All_XOs_PAX7_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C7XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C15XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C8XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C9XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C2XO"), "perc_PAX7"]
wilcox.test(All_XOs_PAX7_CHIR, All_Euploids_PAX7_CHIR)
#p=0.0004
fXOs_PAX7_CHIR <- fXOs_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C8XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C9XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C2XO"), "perc_PAX7"]
wilcox.test(fXOs_PAX7_CHIR, C19C23_PAX7_CHIR)
#p=0.5
#SOX10
SOX10_fem <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Female") %>%
filter(Cell_Line != "C6XX")
SOX10_fem$Cell_Line <- factor(SOX10_fem$Cell_Line, levels = c( "C19XX", "C23XX", "C2XO", "C8XO", "C9XO"))
bp_fem_SOX10 <- ggplot(SOX10_fem, aes(Cell_Line, perc_SOX10, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype)) + scale_color_manual(values = c("violet", "purple")) +
theme(text=element_text(size=5)) +
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent SOX10+")
bp_fem_SOX10
ggsave("SOX10_CHIR_female.pdf", width = 2.5, height = 1.6)
SOX10_male1 <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Male1")
SOX10_male1$Cell_Line <- factor(SOX10_male1$Cell_Line, levels = c("XY", "XO"))
bp_male1_SOX10 <- ggplot(SOX10_male1, aes(Cell_Line, perc_SOX10, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype)) + scale_color_manual(values = c("deepskyblue", "blue")) +
theme(text=element_text(size=5)) +
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent SOX10+")
bp_male1_SOX10
ggsave("SOX10_CHIR_male1.pdf", width = 2.5, height = 1.6)
SOX10_male2 <- IF_percent_PAX7SOX10_CHIR %>% filter(donor=="Male2")
SOX10_male2$Cell_Line <- factor(SOX10_male2$Cell_Line, levels = c("C21XY", "C69XY", "C70XY", "C85XY", "C7XO", "C15XO"))
bp_male2_SOX10 <- ggplot(SOX10_male2, aes(Cell_Line, perc_SOX10, color = condition )) +
facet_wrap(vars (donor), nrow = 1) +
geom_point(size = 1, aes(color = condition, shape = karyotype)) + scale_color_manual(values = c("springgreen", "darkgreen")) +
theme(text=element_text(size=5)) + #change font size of all text
stat_summary(fun.y=median,
geom="crossbar", width=0.5) + ylim(c(0, 100)) + ylab("Percent SOX10+")
bp_male2_SOX10
ggsave("SOX10_CHIR_male2.pdf", width = 2.5, height = 1.6)
XY_SOX10_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="XY"), "perc_SOX10"]
XO_SOX10_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="XO"), "perc_SOX10"]
wilcox.test(XY_SOX10_CHIR, XO_SOX10_CHIR)
#p=0.0012
fXOs_SOX10_CHIR <- fXOs_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C8XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C9XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C2XO"), "perc_SOX10"]
wilcox.test(fXOs_SOX10_CHIR, C19C23_SOX10_CHIR)
#p=0.7
C21C69C70C85_PAX7_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C21XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C69XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C70XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C85XY"), "perc_SOX10"]
C7C15_PAX7_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C7XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C15XO"), "perc_SOX10"]
wilcox.test(C21C69C70C85_PAX7_CHIR, C7C15_PAX7_CHIR)
#p= 9.8e-06
All_Euploids_SOX10_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C21XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C69XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C70XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C85XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="XY" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C19XX" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C23XX"), "perc_SOX10"]
All_XOs_SOX10_CHIR <- IF_percent_PAX7SOX10_CHIR[which(IF_percent_PAX7SOX10_CHIR$Cell_Line=="C7XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C15XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C8XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C9XO" |
IF_percent_PAX7SOX10_CHIR$Cell_Line=="C2XO"), "perc_SOX10"]
wilcox.test(All_XOs_SOX10_CHIR, All_Euploids_SOX10_CHIR)
#p=7.7e-06