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rough-draft_run-analyses_GO.R
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#!/usr/bin/env Rscript
# rough-draft_run-analyses_GO.R
# KA
suppressMessages(library(tidyverse))
# Initialize functions, ggplots themes =======================================
load_panther_results <- function(file) {
df <- readr::read_tsv(
file, skip = 11, show_col_types = FALSE
)
return(df)
}
plot_top_terms_pantherdb <- function(df, top_n) {
# Perform debugging
run <- FALSE
if(base::isTRUE(run)) {
top_n <- 15
df <- BP_PC1_pos_100
}
p <- df %>%
dplyr::mutate(q = -log10(`upload_1 (FDR)`)) %>%
dplyr::rename(GO_BP = `GO biological process complete`) %>%
dplyr::arrange(desc(q)) %>%
dplyr::slice_head(n = top_n) %>%
ggplot2::ggplot(aes(x = reorder(GO_BP, q), y = q)) +
geom_bar(stat = "identity") +
coord_flip() +
xlab("GO BP") +
ylab("-log10(q)") +
ggtitle(paste(
"GO BP:",
deparse(substitute(df)) %>%
gsub("df_", "", .) %>%
gsub("_", ", ", .) %>%
gsub("BP, ", "", .)
)) +
theme_slick
return(p)
}
load_yeastmine_results <- function(file) {
df <- readr::read_tsv(
file,
col_names = c("term", "q_BH", "features", "n_GO"),
show_col_types = FALSE
)
return(df)
}
plot_top_terms_YeastMine <- function(df, top_n) {
# Perform debugging
run <- FALSE
if(base::isTRUE(run)) {
top_n <- 15
df <- group_1
}
p <- df %>%
dplyr::mutate(q = -log10(q_BH)) %>%
dplyr::arrange(desc(q)) %>%
dplyr::slice_head(n = top_n) %>%
ggplot2::ggplot(aes(x = reorder(term, q), y = q)) +
geom_bar(stat = "identity") +
coord_flip() +
xlab("") +
ylab("-log10(q)") +
ggtitle(paste(
"GO terms:",
deparse(substitute(df)) %>%
gsub("df_", "", .) %>%
gsub("_", ", ", .) %>%
gsub("BP, ", "", .)
)) +
theme_minimal()
return(p)
}
# Load custom ggplot2 themes -------------------------------------------------
theme_slick <- theme_classic() +
theme(
panel.grid.major = ggplot2::element_line(linewidth = 0.4),
panel.grid.minor = ggplot2::element_line(linewidth = 0.2),
axis.line = ggplot2::element_line(linewidth = 0.2),
axis.ticks = ggplot2::element_line(linewidth = 0.4),
axis.text = ggplot2::element_text(color = "black"),
axis.title.x = ggplot2::element_text(),
axis.title.y = ggplot2::element_text(),
plot.title = ggplot2::element_text(),
text = element_text(family = "")
)
theme_AG <- theme_classic() +
theme(
panel.grid.major = ggplot2::element_line(linewidth = 3),
panel.grid.minor = ggplot2::element_line(linewidth = 2),
axis.line = ggplot2::element_line(linewidth = 0.5),
axis.ticks = ggplot2::element_line(linewidth = 1.0),
axis.text = ggplot2::element_text(
color = "black", size = 20, face = "bold"
),
axis.title.x = ggplot2::element_text(size = 25, face = "bold"),
axis.title.y = ggplot2::element_text(size = 25, face = "bold"),
plot.title = ggplot2::element_text(size = 20),
text = element_text(family = "")
)
theme_AG_boxed <- theme_AG +
theme(
axis.line = ggplot2::element_line(linewidth = 0),
panel.border = element_rect(linewidth = 2, color = "black", fill = NA)
)
theme_slick_no_legend <- theme_slick + theme(legend.position = "none")
theme_AG_no_legend <- theme_AG + theme(legend.position = "none")
theme_AG_boxed_no_legend <- theme_AG_boxed + theme(legend.position = "none")
# Get situated, load counts matrix ===========================================
if(stringr::str_detect(getwd(), "kalavattam")) {
p_base <- "/Users/kalavattam/Dropbox/FHCC"
} else {
p_base <- "/Users/kalavatt/projects-etc"
}
p_exp <- "2022-2023_RRP6-NAB3/results/2023-0215"
# Set work dir
paste(p_base, p_exp, sep = "/") %>% setwd()
# getwd()
p_GO <- "notebook/KA.2023-0626-0627.PCA-GO-TPM_Ovation"
f_pre <- "PCA.2023-0625__Ovation__mRNA.feature-list-"
f_suf <- ".YeastMine-GO.tsv"
run <- FALSE
if(base::isTRUE(run)) dir.exists(p_GO)
# GO using top 100 features
run <- FALSE
if(base::isTRUE(run)) {
f_PC1_pos_BP_100 <- paste0(f_pre, "100.PC1-pos", f_suf)
f_PC2_pos_BP_100 <- paste0(f_pre, "100.PC2-pos", f_suf)
f_PC3_pos_BP_100 <- paste0(f_pre, "100.PC3-pos", f_suf)
f_PC1_neg_BP_100 <- paste0(f_pre, "100.PC1-neg", f_suf)
f_PC2_neg_BP_100 <- paste0(f_pre, "100.PC2-neg", f_suf)
f_PC3_neg_BP_100 <- paste0(f_pre, "100.PC3-neg", f_suf)
}
# GO using top 200 features
run <- FALSE
if(base::isTRUE(run)) {
f_PC1_pos_BP_200 <- paste0(f_pre, "200.PC1-pos", f_suf)
f_PC2_pos_BP_200 <- paste0(f_pre, "200.PC2-pos", f_suf)
f_PC3_pos_BP_200 <- paste0(f_pre, "200.PC3-pos", f_suf)
f_PC1_neg_BP_200 <- paste0(f_pre, "200.PC1-neg", f_suf)
f_PC2_neg_BP_200 <- paste0(f_pre, "200.PC2-neg", f_suf)
f_PC3_neg_BP_200 <- paste0(f_pre, "200.PC3-neg", f_suf)
}
# GO using top 500 features
run <- TRUE
if(base::isTRUE(run)) {
f_PC1_pos_BP_500 <- paste0(f_pre, "500.PC1-pos", f_suf)
f_PC2_pos_BP_500 <- paste0(f_pre, "500.PC2-pos", f_suf)
f_PC3_pos_BP_500 <- paste0(f_pre, "500.PC3-pos", f_suf)
f_PC1_neg_BP_500 <- paste0(f_pre, "500.PC1-neg", f_suf)
f_PC2_neg_BP_500 <- paste0(f_pre, "500.PC2-neg", f_suf)
f_PC3_neg_BP_500 <- paste0(f_pre, "500.PC3-neg", f_suf)
}
# Panther, 100 features
run <- FALSE
if(base::isTRUE(run)) {
BP_PC1_pos_100 <- load_yeastmine_results(
paste(p_GO, f_PC1_pos_BP_100, sep = "/")
)
BP_PC1_neg_100 <- load_yeastmine_results(
paste(p_GO, f_PC1_neg_BP_100, sep = "/")
)
BP_PC2_pos_100 <- load_yeastmine_results(
paste(p_GO, f_PC2_pos_BP_100, sep = "/")
)
BP_PC2_neg_100 <- load_yeastmine_results(
paste(p_GO, f_PC2_neg_BP_100, sep = "/")
)
BP_PC3_pos_100 <- load_yeastmine_results(
paste(p_GO, f_PC3_pos_BP_100, sep = "/")
)
BP_PC3_neg_100 <- load_yeastmine_results(
paste(p_GO, f_PC3_neg_BP_100, sep = "/")
)
}
# Panther, 200 features
run <- FALSE
if(base::isTRUE(run)) {
BP_PC1_pos_200 <- load_yeastmine_results(
paste(p_GO, f_PC1_pos_BP_200, sep = "/")
)
BP_PC1_neg_200 <- load_yeastmine_results(
paste(p_GO, f_PC1_neg_BP_200, sep = "/")
)
BP_PC2_pos_200 <- load_yeastmine_results(
paste(p_GO, f_PC2_pos_BP_200, sep = "/")
)
BP_PC2_neg_200 <- load_yeastmine_results(
paste(p_GO, f_PC2_neg_BP_200, sep = "/")
)
BP_PC3_pos_200 <- load_yeastmine_results(
paste(p_GO, f_PC3_pos_BP_200, sep = "/")
)
BP_PC3_neg_200 <- load_yeastmine_results(
paste(p_GO, f_PC3_neg_BP_200, sep = "/")
)
}
# Panther, 500 features
# run <- TRUE
# if(base::isTRUE(run)) {
if(file.exists(paste(p_GO, f_PC1_pos_BP_500, sep = "/"))) {
BP_PC1_pos_500 <- load_yeastmine_results(
paste(p_GO, f_PC1_pos_BP_500, sep = "/")
)
} else {
paste("File does not exists", paste(p_GO, f_PC1_pos_BP_500, sep = "/"))
}
if(file.exists(paste(p_GO, f_PC1_neg_BP_500, sep = "/"))) {
BP_PC1_neg_500 <- load_yeastmine_results(
paste(p_GO, f_PC1_neg_BP_500, sep = "/")
)
} else {
paste("File does not exists", paste(p_GO, f_PC1_neg_BP_500, sep = "/"))
}
if(file.exists(paste(p_GO, f_PC2_pos_BP_500, sep = "/"))) {
BP_PC2_pos_500 <- load_yeastmine_results(
paste(p_GO, f_PC2_pos_BP_500, sep = "/")
)
} else {
paste("File does not exists", paste(p_GO, f_PC2_pos_BP_500, sep = "/"))
}
if(file.exists(paste(p_GO, f_PC2_neg_BP_500, sep = "/"))) {
BP_PC2_neg_500 <- load_yeastmine_results(
paste(p_GO, f_PC2_neg_BP_500, sep = "/")
)
} else {
paste("File does not exists", paste(p_GO, f_PC2_neg_BP_500, sep = "/"))
}
if(file.exists(paste(p_GO, f_PC3_pos_BP_500, sep = "/"))) {
BP_PC3_pos_500 <- load_yeastmine_results(
paste(p_GO, f_PC3_pos_BP_500, sep = "/")
)
} else {
paste("File does not exists", paste(p_GO, f_PC3_pos_BP_500, sep = "/"))
}
if(file.exists(paste(p_GO, f_PC3_neg_BP_500, sep = "/"))) {
BP_PC3_neg_500 <- load_yeastmine_results(
paste(p_GO, f_PC3_neg_BP_500, sep = "/")
)
} else {
paste("File does not exists", paste(p_GO, f_PC3_neg_BP_500, sep = "/"))
}
# }
top_n <- 15
run <- TRUE
if(base::isTRUE(run)) {
# bars_BP_PC1_neg_100 <- plot_top_terms_YeastMine(BP_PC1_neg_100, top_n)
# bars_BP_PC1_neg_200 <- plot_top_terms_YeastMine(BP_PC1_neg_200, top_n)
bars_BP_PC1_neg_500 <- plot_top_terms_YeastMine(BP_PC1_neg_500, top_n)
# bars_BP_PC2_neg_100 <- plot_top_terms_YeastMine(BP_PC2_neg_100, top_n)
# bars_BP_PC2_neg_200 <- plot_top_terms_YeastMine(BP_PC2_neg_200, top_n)
# bars_BP_PC2_neg_500 <- plot_top_terms_YeastMine(BP_PC2_neg_500, top_n) #DOESNOTEXIST
# bars_BP_PC3_neg_100 <- plot_top_terms_YeastMine(BP_PC3_neg_100, top_n)
# bars_BP_PC3_neg_200 <- plot_top_terms_YeastMine(BP_PC3_neg_200, top_n)
bars_BP_PC3_neg_500 <- plot_top_terms_YeastMine(BP_PC3_neg_500, top_n)
# bars_BP_PC1_pos_100 <- plot_top_terms_YeastMine(BP_PC1_pos_100, top_n)
# bars_BP_PC1_pos_200 <- plot_top_terms_YeastMine(BP_PC1_pos_200, top_n)
bars_BP_PC1_pos_500 <- plot_top_terms_YeastMine(BP_PC1_pos_500, top_n)
# bars_BP_PC2_pos_100 <- plot_top_terms_YeastMine(BP_PC2_pos_100, top_n)
# bars_BP_PC2_pos_200 <- plot_top_terms_YeastMine(BP_PC2_pos_200, top_n)
bars_BP_PC2_pos_500 <- plot_top_terms_YeastMine(BP_PC2_pos_500, top_n)
# bars_BP_PC3_pos_100 <- plot_top_terms_YeastMine(BP_PC3_pos_100, top_n)
# bars_BP_PC3_pos_200 <- plot_top_terms_YeastMine(BP_PC3_pos_200, top_n)
bars_BP_PC3_pos_500 <- plot_top_terms_YeastMine(BP_PC3_pos_500, top_n)
}
run <- TRUE
if(base::isTRUE(run)) {
# print(bars_BP_PC1_neg_100)
# print(bars_BP_PC2_neg_100)
# print(bars_BP_PC3_neg_100)
#
# print(bars_BP_PC1_neg_200)
# print(bars_BP_PC2_neg_200)
# print(bars_BP_PC3_neg_200)
#
# print(bars_BP_PC1_neg_500)
# print(bars_BP_PC2_neg_500)
# print(bars_BP_PC3_neg_500)
# print(bars_BP_PC1_neg_100)
# print(bars_BP_PC1_neg_200)
print(bars_BP_PC1_neg_500)
# print(bars_BP_PC2_neg_100)
# print(bars_BP_PC2_neg_200)
# print(bars_BP_PC2_neg_500) #DOESNOTEXIST
# print(bars_BP_PC3_neg_100)
# print(bars_BP_PC3_neg_200)
print(bars_BP_PC3_neg_500)
# print(bars_BP_PC1_pos_100)
# print(bars_BP_PC2_pos_100)
# print(bars_BP_PC3_pos_100)
#
# print(bars_BP_PC1_pos_200)
# print(bars_BP_PC2_pos_200)
# print(bars_BP_PC3_pos_200)
#
# print(bars_BP_PC1_pos_500)
# print(bars_BP_PC2_pos_500)
# print(bars_BP_PC3_pos_500)
# print(bars_BP_PC1_pos_100)
# print(bars_BP_PC1_pos_200)
print(bars_BP_PC1_pos_500)
# print(bars_BP_PC2_pos_100)
# print(bars_BP_PC2_pos_200)
print(bars_BP_PC2_pos_500)
# print(bars_BP_PC3_pos_100)
# print(bars_BP_PC3_pos_200)
print(bars_BP_PC3_pos_500)
}
# Save PC1 results
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC1_pos_100)), ".png"),
# bars_BP_PC1_pos_100
# )
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC1_pos_200)), ".png"),
# bars_BP_PC1_pos_200
# )
ggsave(
paste0(getwd(), "/", deparse(substitute(bars_BP_PC1_pos_500)), ".png"),
bars_BP_PC1_pos_500
)
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC1_neg_100)), ".png"),
# bars_BP_PC1_neg_100
# )
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC1_neg_200)), ".png"),
# bars_BP_PC1_neg_200
# )
ggsave(
paste0(getwd(), "/", deparse(substitute(bars_BP_PC1_neg_500)), ".png"),
bars_BP_PC1_neg_500
)
# Save PC2 results
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC2_pos_100)), ".png"),
# bars_BP_PC2_pos_100
# )
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC2_pos_200)), ".png"),
# bars_BP_PC2_pos_200
# )
ggsave(
paste0(getwd(), "/", deparse(substitute(bars_BP_PC2_pos_500)), ".png"),
bars_BP_PC2_pos_500
)
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC2_neg_100)), ".png"),
# bars_BP_PC2_neg_100
# )
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC2_neg_200)), ".png"),
# bars_BP_PC2_neg_200
# )
# ggsave(
# paste0(getwd(), "/", deparse(substitute(bars_BP_PC2_neg_500)), ".png"),
# bars_BP_PC2_neg_500
# ) #DOESNOTEXIST
ggsave(
paste0(getwd(), "/", deparse(substitute(bars_BP_PC3_pos_500)), ".png"),
bars_BP_PC3_pos_500
)
ggsave(
paste0(getwd(), "/", deparse(substitute(bars_BP_PC3_neg_500)), ".png"),
bars_BP_PC3_neg_500
)