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GSEA_Figures.R
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GSEA_Figures.R
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library(ggplot2)
top_go = read.csv("C:/Users/jonan/Documents/Tyseq/Data/ForReview/Top_GSEA_Pathways_GO_filtered.csv")
top_kegg = read.csv("C:/Users/jonan/Documents/Tyseq/Data/ForReview/Top_GSEA_Pathways_KEGG.csv")
fig_width= 10
fig_height = 7
#####
#-----------------------------------------------------------------------------#
# HEAT MAP - GO
#-----------------------------------------------------------------------------#
# Summarize pathway information and create negative log p value variable for graphing
path_go <- top_go %>% filter(pval <= 0.1)
path_go <- path_go %>% mutate(neglogpvalue = -log10(pval))
# Graph pathways by p value
pathfig_go <- ggplot(path_go, aes(x = reorder(pathway, neglogpvalue), y = neglogpvalue)) +
# Conditionally set fill color based on the "ES" value
geom_bar(aes(fill = ifelse(ES < 0, "red", "black")), stat = "identity") +
coord_flip() +
scale_x_discrete(name = "GO Biological Processes Associated with Diabetes") +
scale_fill_identity() + # Ensure the colors are applied as specified
ylab("-log(p value)") +
theme(axis.text.x = element_text(face = "bold", size = 10, angle = 0),
axis.text.y = element_text(face = "bold", size = 10, angle = 0))
# Save the figure with increased width (e.g., width = fig_width inches)
# ggsave("C:/Users/jonan/Documents/Tyseq/Figures/Up-Down_GO_pathways.png", width = 12)
ggsave("../Figures/Up-Down_GO_pathways.png",
plot = pathfig_go,
width = fig_width,
height = fig_height,
dpi = 600)
ggsave("../Figures/Up-Down_GO_pathways.pdf",
plot = pathfig_go,
width = fig_width,
height = fig_height,
dpi = 600)
#####
#-----------------------------------------------------------------------------#
# HEAT MAP - KEGG
#-----------------------------------------------------------------------------#
# Summarize pathway information and create negative log p value variable for graphing
path_go <- top_kegg %>% filter(pval <= 0.1)
path_go <- path_go %>% mutate(neglogpvalue = -log10(pval))
# Graph pathways by p value
pathfig_kegg <- ggplot(path_go, aes(x = reorder(pathway, neglogpvalue), y = neglogpvalue)) +
# Conditionally set fill color based on the "ES" value
geom_bar(aes(fill = ifelse(ES < 0, "red", "black")), stat = "identity") +
coord_flip() +
scale_x_discrete(name = "KEGG Biological Processes Associated with Diabetes") +
scale_fill_identity() + # Ensure the colors are applied as specified
ylab("-log(p value)") +
theme(axis.text.x = element_text(face = "bold", size = 10, angle = 0),
axis.text.y = element_text(face = "bold", size = 10, angle = 0))
# Save the figure with increased width (e.g., width = fig_width inches)
ggsave("C:/Users/jonan/Documents/Tyseq/Figures/Up-Down_KEGG_pathways.png",
plot = pathfig_kegg,
width = fig_width,
height = fig_height,
dpi = 600)
ggsave("C:/Users/jonan/Documents/Tyseq/Figures/Up-Down_KEGG_pathways.pdf",
plot = pathfig_kegg,
width = fig_width,
height = fig_height,
dpi = 600)