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plots.R
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plots.R
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# This script generates plots from the paper
# Author: Mustafa S. Pir
source("data_wrangling.R")
#windowsFonts("Open Sans SemiBold" = windowsFont("Open Sans SemiBold"))
# Dyf assay (head)
ggplot(data_head_plot, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("Dyf Assay (Head)") +
theme(text = element_text(family = "Open Sans SemiBold"))
# Dyf assay (tail)
ggplot(data_tail_plot, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("Dyf Assay (Tail)") +
theme(text = element_text(family = "Open Sans SemiBold"))
# Dyf assay head 2
ggplot(data2_head_plot, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("Dyf Assay (Head)") +
theme(text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.4))
# Dyf assay tail 2
ggplot(data2_tail_plot, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("Dyf Assay (Tail)") +
theme(text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.4))
# AWB cilia morphology
ggplot(morphology1, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7,9)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("AWB Cilia Morphology") +
theme(text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.4))
# AWB cilia morphology 2
ggplot(morphology2, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7,9)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("AWB Cilia Morphology") +
theme(text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.4))
# Short cilia length
ggplot(length_short1, aes(x = Genotype, y = Length, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
coord_flip() +
ylab("Length(um)") +
ggtitle("Short Cilia Length") +
theme(legend.position = "none", text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.25))
# Long cilia length
ggplot(length_long1, aes(x = Genotype, y = Length, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
coord_flip() +
ylab("Length(um)") +
ggtitle("Long Cilia Length") +
theme(legend.position = "none", text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.25))
# Short cilia length 2
ggplot(lengthx_short1, aes(x = Genotype, y = Length, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
ylab("Length(um)") +
ggtitle("Short Cilia Length") +
theme(legend.position = "none", text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.5))
# Long cilia length 2
ggplot(lengthx_long1, aes(x = Genotype, y = Length, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
ylab("Length(um)") +
ggtitle("Long Cilia Length") +
theme(legend.position = "none", text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.5))
# Short cilia length 2
ggplot(gcy_length1, aes(x = Genotype, y = Length, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
coord_flip() +
ylab("Length(um)") +
ggtitle("ASER Cilia Length") +
theme(legend.position = "none", text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.35))
# Short cilia length 2
ggplot(srb6_length1, aes(x = Genotype, y = Length, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
coord_flip() +
ylab("Length(um)") +
ggtitle("PHA/PHB Cilia Length") +
theme(legend.position = "none", text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.35))
# Short cilia awb_length
ggplot(awb_length1, aes(x = Genotype, y = length, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
coord_flip() +
ylab("Length(um)") +
ggtitle("AWB Cilia Length (short)") +
theme(legend.position = "none", text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.35))
# IFT figures
ggplot(ift[ift$IFT == "Anterograde" & ift$Marker != "BBS-7::GFP",], aes(x = Marker, y = Number.of.Particles, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
#geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
#geom_boxplot(outlier.shape = NA) +
#scale_color_brewer(palette = "Paired") +
#scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
#coord_flip() +
ylab("Number of Particles") +
ggtitle("Anterograde") +
theme(legend.position = "right", text = element_text(family = "Open Sans SemiBold", size = 12),
plot.title = element_text(hjust = 0.6))
ggplot(ift[ift$IFT == "Retrograde" & ift$Marker != "BBS-7::GFP",], aes(x = Marker, y = Number.of.Particles, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
#geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
#geom_boxplot(outlier.shape = NA) +
#scale_color_brewer(palette = "Paired") +
#scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
#coord_flip() +
ylab("Number of Particles") +
ggtitle("Retrograde") +
theme(legend.position = "right", text = element_text(family = "Open Sans SemiBold", size = 12),
plot.title = element_text(hjust = 0.6))
ggplot(ift[ift$IFT == "Anterograde" & ift$Marker == "BBS-7::GFP",], aes(x = Marker, y = Number.of.Particles, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
#geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
#geom_boxplot(outlier.shape = NA) +
#scale_color_brewer(palette = "Paired") +
#scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
#coord_flip() +
ylab("Number of Particles") +
ggtitle("Anterograde") +
theme(legend.position = "right", text = element_text(family = "Open Sans SemiBold", size = 12),
plot.title = element_text(hjust = 0.6))
ggplot(ift[ift$IFT == "Retrograde" & ift$Marker == "BBS-7::GFP",], aes(x = Marker, y = Number.of.Particles, fill = Genotype)) +
geom_boxplot(outlier.shape = NA) +
#geom_jitter(shape=16, position=position_jitter(0.2), size = 1) +
#geom_boxplot(outlier.shape = NA) +
#scale_color_brewer(palette = "Paired") +
#scale_fill_manual(values = rep(prpls[5],11)) +
theme_minimal() +
#coord_flip() +
ylab("Number of Particles") +
ggtitle("Retrograde") +
theme(legend.position = "right", text = element_text(family = "Open Sans SemiBold", size = 12),
plot.title = element_text(hjust = 0.6))
# AWB cilia morphology
ggplot(morphologyn1, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7,9)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("AWB Cilia Morphology") +
theme(text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.4))
ggsave("awb_morphology.jpg", width = 11, height = 7, dpi = 300)
ggplot(morphologym1, aes(x = Genotype, y = Count)) +
geom_bar(aes(color = Phenotype, fill = Phenotype),
stat = "identity", position = position_stack(), width = 0.8) +
scale_fill_manual(values = prpls[c(3,5,7,9)]) +
scale_color_brewer() +
theme_classic() +
coord_flip() +
ylab("Count(%)") +
ggtitle("AWB Cilia Morphology") +
theme(text = element_text(family = "Open Sans SemiBold"),
plot.title = element_text(hjust = 0.4))
ggsave("awb_morphology2.jpg", width = 9, height = 7, dpi = 300)