Correlation Heatmap of Sample
Sayan Paul
2025-05-22
Last updated: 2025-05-22
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Knit directory: CX5461_Project/
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| Rmd | e3ba601 | sayanpaul01 | 2025-02-02 | Added Correlation Heatmap of Samples |
📌 Correlation Heatmap of Samples
This analysis generates Pearson and Spearman correlation heatmaps to explore relationships between RNA-seq samples.
📌 Load Required Libraries
# Load required libraries
library(ComplexHeatmap)Warning: package 'ComplexHeatmap' was built under R version 4.3.1library(circlize) # For color mappingWarning: package 'circlize' was built under R version 4.3.3library(dplyr)Warning: package 'dplyr' was built under R version 4.3.2library(edgeR)Warning: package 'edgeR' was built under R version 4.3.2Warning: package 'limma' was built under R version 4.3.1library(ggplot2)
library(reshape2)
library(Biobase)Warning: package 'Biobase' was built under R version 4.3.1Warning: package 'BiocGenerics' was built under R version 4.3.1library(limma)
library(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 'stringr' was built under R version 4.3.2Warning: package 'lubridate' was built under R version 4.3.3library(scales)Warning: package 'scales' was built under R version 4.3.2library(biomaRt)Warning: package 'biomaRt' was built under R version 4.3.2library(ggrepel)Warning: package 'ggrepel' was built under R version 4.3.3library(corrplot)Warning: package 'corrplot' was built under R version 4.3.3library(Hmisc)Warning: package 'Hmisc' was built under R version 4.3.3library(org.Hs.eg.db)Warning: package 'AnnotationDbi' was built under R version 4.3.2Warning: package 'IRanges' was built under R version 4.3.1Warning: package 'S4Vectors' was built under R version 4.3.2library(AnnotationDbi)
library(tidyr)
library(ggfortify)📍 Load Count Matrix
📌Data Preparation
# Ensure the correct column names are assigned
lcpm_2 <- filcpm_matrix
colnames(lcpm_2) <- Metadata$Sample_name
# Compute correlation matrices
cor_matrix_pearson <- cor(lcpm_2, method = "pearson")
cor_matrix_spearman <- cor(lcpm_2, method = "spearman")
# Extract metadata columns
individuals <- as.character(Metadata$Ind)
timepoints <- as.character(Metadata$Time)
drugs <- as.character(Metadata$Drug)
concentrations <- as.character(Metadata$Conc.)
sex <- as.character(Metadata$Sex)
# Define color palettes for annotations
ind_colors <- c("1" = "red", "2" = "blue", "3" = "green", "4" = "orange", "5" = "thistle", "6" = "magenta4")
time_colors <- c("3" = "purple", "24" = "pink", "48" = "tomato3")
drug_colors <- c("CX-5461" = "yellow", "DOX" = "magenta4", "VEH" = "red3")
conc_colors <- c("0.1" = "lightblue", "0.5" = "lightcoral")
sex_colors <- c("Male" = "skyblue3", "Female" = "deeppink3")
# Create annotations
top_annotation <- HeatmapAnnotation(
individuals = individuals,
sex = sex, # New annotation
timepoints = timepoints,
drugs = drugs,
concentrations = concentrations,
col = list(
individuals = ind_colors,
sex = sex_colors, # Link sex to palette
timepoints = time_colors,
drugs = drug_colors,
concentrations = conc_colors
),
annotation_legend_param = list(
sex = list(title = "Sex"),
individuals = list(title = "Individual"),
timepoints = list(title = "Time"),
drugs = list(title = "Drug"),
concentrations = list(title = "Concentration")
)
)📌Pearson Correlation Heatmap
# Generate the heatmap with annotations (Pearson Correlation)
heatmap_pearson <- Heatmap(cor_matrix_pearson,
name = "Pearson Correlation",
top_annotation = top_annotation,
show_row_names = TRUE,
show_column_names = TRUE,
cluster_rows = TRUE,
cluster_columns = TRUE)
# Draw the heatmap
draw(heatmap_pearson)
📌Spearman Correlation Heatmap
# Generate the heatmap with annotations (Spearman Correlation)
heatmap_spearman <- Heatmap(cor_matrix_spearman,
name = "Spearman Correlation",
top_annotation = top_annotation,
show_row_names = TRUE,
show_column_names = TRUE,
cluster_rows = TRUE,
cluster_columns = TRUE)
# Draw the heatmap
draw(heatmap_spearman)
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 grid stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ggfortify_0.4.17 org.Hs.eg.db_3.18.0 AnnotationDbi_1.64.1
[4] IRanges_2.36.0 S4Vectors_0.40.2 Hmisc_5.2-3
[7] corrplot_0.95 ggrepel_0.9.6 biomaRt_2.58.2
[10] scales_1.3.0 lubridate_1.9.4 forcats_1.0.0
[13] stringr_1.5.1 purrr_1.0.4 readr_2.1.5
[16] tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0
[19] Biobase_2.62.0 BiocGenerics_0.48.1 reshape2_1.4.4
[22] ggplot2_3.5.2 edgeR_4.0.16 limma_3.58.1
[25] dplyr_1.1.4 circlize_0.4.16 ComplexHeatmap_2.18.0
[28] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9 gridExtra_2.3
[4] rlang_1.1.3 magrittr_2.0.3 clue_0.3-66
[7] GetoptLong_1.0.5 git2r_0.36.2 matrixStats_1.5.0
[10] compiler_4.3.0 RSQLite_2.3.9 getPass_0.2-4
[13] png_0.1-8 callr_3.7.6 vctrs_0.6.5
[16] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[19] fastmap_1.2.0 magick_2.8.6 backports_1.5.0
[22] dbplyr_2.5.0 XVector_0.42.0 promises_1.3.2
[25] rmarkdown_2.29 tzdb_0.5.0 ps_1.8.1
[28] bit_4.6.0 xfun_0.52 zlibbioc_1.48.2
[31] cachem_1.1.0 GenomeInfoDb_1.38.8 jsonlite_2.0.0
[34] progress_1.2.3 blob_1.2.4 later_1.3.2
[37] parallel_4.3.0 prettyunits_1.2.0 cluster_2.1.8.1
[40] R6_2.6.1 bslib_0.9.0 stringi_1.8.3
[43] RColorBrewer_1.1-3 rpart_4.1.24 jquerylib_0.1.4
[46] Rcpp_1.0.12 iterators_1.0.14 knitr_1.50
[49] base64enc_0.1-3 nnet_7.3-20 httpuv_1.6.15
[52] timechange_0.3.0 tidyselect_1.2.1 rstudioapi_0.17.1
[55] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20
[58] curl_6.2.2 processx_3.8.6 lattice_0.22-7
[61] plyr_1.8.9 withr_3.0.2 KEGGREST_1.42.0
[64] evaluate_1.0.3 foreign_0.8-90 BiocFileCache_2.10.2
[67] xml2_1.3.8 Biostrings_2.70.3 filelock_1.0.3
[70] pillar_1.10.2 whisker_0.4.1 checkmate_2.3.2
[73] foreach_1.5.2 generics_0.1.3 rprojroot_2.0.4
[76] RCurl_1.98-1.17 hms_1.1.3 munsell_0.5.1
[79] glue_1.7.0 tools_4.3.0 data.table_1.17.0
[82] locfit_1.5-9.12 fs_1.6.3 XML_3.99-0.18
[85] Cairo_1.6-2 colorspace_2.1-0 GenomeInfoDbData_1.2.11
[88] htmlTable_2.4.3 Formula_1.2-5 cli_3.6.1
[91] rappdirs_0.3.3 gtable_0.3.6 sass_0.4.10
[94] digest_0.6.34 htmlwidgets_1.6.4 rjson_0.2.23
[97] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4
[100] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0
[103] bit64_4.6.0-1