Figure_S9
Last updated: 2025-08-10
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Knit directory: Paul_CX_2025/
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📌 Differential Gene Expression Analysis
📌 Load Required Libraries
# Load necessary packages
library(edgeR)Warning: package 'edgeR' was built under R version 4.3.2Warning: package 'limma' was built under R version 4.3.1library(limma)
library(data.table)Warning: package 'data.table' was built under R version 4.3.3library(tidyverse)Warning: package 'tidyverse' was built under R version 4.3.2Warning: package 'tidyr' was built under R version 4.3.3Warning: package 'readr' was built under R version 4.3.3Warning: package 'purrr' was built under R version 4.3.3Warning: package 'dplyr' was built under R version 4.3.2Warning: package 'stringr' was built under R version 4.3.2Warning: package 'lubridate' was built under R version 4.3.3library(ggplot2)
library(dplyr)
library(scales)Warning: package 'scales' was built under R version 4.3.2library(biomaRt)Warning: package 'biomaRt' was built under R version 4.3.2library(Homo.sapiens)Warning: package 'AnnotationDbi' was built under R version 4.3.2Warning: package 'BiocGenerics' was built under R version 4.3.1Warning: package 'Biobase' was built under R version 4.3.1Warning: package 'IRanges' was built under R version 4.3.1Warning: package 'S4Vectors' was built under R version 4.3.2Warning: package 'OrganismDbi' was built under R version 4.3.1Warning: package 'GenomicFeatures' was built under R version 4.3.3Warning: package 'GenomeInfoDb' was built under R version 4.3.3Warning: package 'GenomicRanges' was built under R version 4.3.1📌 Volcano Plots for Differential Expression Analysis
library(ggplot2)
# Function to generate volcano plot with counts in legend
generate_volcano_plot <- function(toptable, title) {
# Annotate significance
toptable$Significance <- "Not Significant"
toptable$Significance[toptable$logFC > 0 & toptable$adj.P.Val < 0.05] <- "Upregulated"
toptable$Significance[toptable$logFC < 0 & toptable$adj.P.Val < 0.05] <- "Downregulated"
# Count per category
count_table <- table(toptable$Significance)
up_count <- count_table["Upregulated"]
down_count <- count_table["Downregulated"]
ns_count <- count_table["Not Significant"]
# Handle missing counts
if (is.na(up_count)) up_count <- 0
if (is.na(down_count)) down_count <- 0
if (is.na(ns_count)) ns_count <- 0
# Labels with counts
custom_labels <- c(
paste0("Downregulated (", down_count, ")"),
paste0("Not Significant (", ns_count, ")"),
paste0("Upregulated (", up_count, ")")
)
names(custom_labels) <- c("Downregulated", "Not Significant", "Upregulated")
# Plot
ggplot(toptable, aes(x = logFC, y = -log10(P.Value), color = Significance)) +
geom_point(alpha = 0.4, size = 2) +
scale_color_manual(
values = c(
"Downregulated" = "red",
"Upregulated" = "blue",
"Not Significant" = "gray"
),
labels = custom_labels
) +
xlim(-5, 5) +
labs(
title = title,
x = "log2 Fold Change",
y = "-log10 P-value",
color = "Gene Status"
) +
theme_bw() +
theme(
legend.position = "right",
plot.title = element_text(size = rel(1.5), hjust = 0.5),
axis.title = element_text(size = rel(1.25)),
legend.title = element_text(size = 11, face = "bold"),
legend.text = element_text(size = 10)
)
}
# Load all Toptable CSV files
deg_files <- list.files("data/DEGs/", pattern = "^Toptable_.*\\.csv$", full.names = TRUE)
# Loop through files and show plots
for (file in deg_files) {
df <- read.csv(file)
plot_title <- gsub("^Toptable_|\\.csv$", "", basename(file))
p <- generate_volcano_plot(df, paste("Volcano Plot:", plot_title))
print(p)
}
Warning: Removed 3 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
Warning: Removed 34 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning: Removed 28 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning: Removed 24 rows containing missing values or values outside the scale range
(`geom_point()`).
sessionInfo()R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 26100)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Homo.sapiens_1.3.1
[2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[3] org.Hs.eg.db_3.18.0
[4] GO.db_3.18.0
[5] OrganismDbi_1.44.0
[6] GenomicFeatures_1.54.4
[7] GenomicRanges_1.54.1
[8] GenomeInfoDb_1.38.8
[9] AnnotationDbi_1.64.1
[10] IRanges_2.36.0
[11] S4Vectors_0.40.2
[12] Biobase_2.62.0
[13] BiocGenerics_0.48.1
[14] biomaRt_2.58.2
[15] scales_1.3.0
[16] lubridate_1.9.4
[17] forcats_1.0.0
[18] stringr_1.5.1
[19] dplyr_1.1.4
[20] purrr_1.0.4
[21] readr_2.1.5
[22] tidyr_1.3.1
[23] tibble_3.2.1
[24] ggplot2_3.5.2
[25] tidyverse_2.0.0
[26] data.table_1.17.0
[27] edgeR_4.0.16
[28] limma_3.58.1
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9
[3] RBGL_1.78.0 rlang_1.1.3
[5] magrittr_2.0.3 git2r_0.36.2
[7] matrixStats_1.5.0 compiler_4.3.0
[9] RSQLite_2.3.9 png_0.1-8
[11] vctrs_0.6.5 pkgconfig_2.0.3
[13] crayon_1.5.3 fastmap_1.2.0
[15] dbplyr_2.5.0 XVector_0.42.0
[17] labeling_0.4.3 Rsamtools_2.18.0
[19] promises_1.3.2 rmarkdown_2.29
[21] tzdb_0.5.0 graph_1.80.0
[23] bit_4.6.0 xfun_0.52
[25] zlibbioc_1.48.2 cachem_1.1.0
[27] jsonlite_2.0.0 progress_1.2.3
[29] blob_1.2.4 later_1.3.2
[31] DelayedArray_0.28.0 BiocParallel_1.36.0
[33] parallel_4.3.0 prettyunits_1.2.0
[35] R6_2.6.1 bslib_0.9.0
[37] stringi_1.8.3 rtracklayer_1.62.0
[39] jquerylib_0.1.4 Rcpp_1.0.12
[41] SummarizedExperiment_1.32.0 knitr_1.50
[43] Matrix_1.6-1.1 httpuv_1.6.15
[45] timechange_0.3.0 tidyselect_1.2.1
[47] abind_1.4-8 rstudioapi_0.17.1
[49] yaml_2.3.10 codetools_0.2-20
[51] curl_6.2.2 lattice_0.22-7
[53] withr_3.0.2 KEGGREST_1.42.0
[55] evaluate_1.0.3 BiocFileCache_2.10.2
[57] xml2_1.3.8 Biostrings_2.70.3
[59] BiocManager_1.30.25 pillar_1.10.2
[61] filelock_1.0.3 MatrixGenerics_1.14.0
[63] generics_0.1.3 rprojroot_2.0.4
[65] RCurl_1.98-1.17 hms_1.1.3
[67] munsell_0.5.1 glue_1.7.0
[69] tools_4.3.0 BiocIO_1.12.0
[71] locfit_1.5-9.12 GenomicAlignments_1.38.2
[73] fs_1.6.3 XML_3.99-0.18
[75] grid_4.3.0 colorspace_2.1-0
[77] GenomeInfoDbData_1.2.11 restfulr_0.0.15
[79] cli_3.6.1 rappdirs_0.3.3
[81] workflowr_1.7.1 S4Arrays_1.2.1
[83] gtable_0.3.6 sass_0.4.10
[85] digest_0.6.34 SparseArray_1.2.4
[87] farver_2.1.2 rjson_0.2.23
[89] memoise_2.0.1 htmltools_0.5.8.1
[91] lifecycle_1.0.4 httr_1.4.7
[93] statmod_1.5.0 bit64_4.6.0-1