Last updated: 2021-09-10

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Knit directory: hesc-epigenomics/

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Rmd 6d126f8 C. Navarro 2021-09-10 wflow_publish(“./analysis/sup_01_replicates.Rmd”, verbose = T)

Summary

This is the supplementary notebook for replicates analysis

Replicates correlation

library(corrplot)
corrplot 0.90 loaded
bins_table <- "./data/meta/Kumar_2020_master_bins_10kb_table_final_raw.tsv"

bins_df <- read.table(bins_table, sep = "\t", header = T,
                      colClasses = c("character", "integer", "integer", "factor", "factor", rep("numeric", 112)))

reps <- bins_df[, grepl("rep[1-3]_mean_cov", colnames(bins_df))]

cormat <- cor(reps, method = "pearson")
corrplot(cormat)

Replicates ChromHMM

H3K4m3

flist <- list.files(bwdir, pattern = "H3K4m3.*rep[1-3].hg38.scaled.bw", full.names = T)

labels <- gsub(".hg38.scaled.bw", "", basename(flist))
labels <- gsub("_H9", "", labels)

chromhmm <- params$chromhmm

plot_bw_loci_summary_heatmap(flist, chromhmm, labels = labels, remove_top=0.001)

H3K27m3

flist <- list.files(bwdir, pattern = "H3K27m3.*rep[1-3].hg38.scaled.bw", full.names = T)

labels <- gsub(".hg38.scaled.bw", "", basename(flist))
labels <- gsub("_H9", "", labels)

chromhmm <- params$chromhmm

plot_bw_loci_summary_heatmap(flist, chromhmm, labels = labels, remove_top=0.001) 

H2Aub

flist <- list.files(bwdir, pattern = "H2Aub.*rep[1-3].hg38.scaled.bw", full.names = T)

labels <- gsub(".hg38.scaled.bw", "", basename(flist))
labels <- gsub("_H9", "", labels)

chromhmm <- params$chromhmm

plot_bw_loci_summary_heatmap(flist, chromhmm, labels = labels, remove_top=0.001)

Replicates at bivalent

H3K4m3

color_list <- c("#278b8b", "#36bfbf", "#1b6363",
                "#76c6c7", "#aed1d1", "#778f8f",
                "#f44b34", "#ba3927", "#872517",
                "#f5baba", "#b88c8c", "#8c6f6f")

plot_bw_profile(flist, labels = labels, colors = color_list, loci = court_genes, upstream = 5000, downstream = 5000, mode = "stretch") + theme_default(base_size = 12) + theme(legend.position = c(0.80, 0.75)) + labs(x = "Court Bivalent 2017")

H3K27m3

color_list <- c("#278b8b", "#36bfbf", "#1b6363",
                "#76c6c7", "#aed1d1", "#778f8f",
                "#f44b34", "#ba3927", "#872517",
                "#f5baba", "#b88c8c", "#8c6f6f")

plot_bw_profile(flist, labels = labels, colors = color_list, loci = court_genes, upstream = 5000, downstream = 5000, mode = "stretch")  + theme_default(base_size = 12) + theme(legend.position = c(0.80, 0.75)) + labs(x = "Court Bivalent 2017")

H2Aub

color_list <- c("#278b8b", "#36bfbf", "#1b6363",
                "#76c6c7", "#aed1d1", "#778f8f",
                "#f44b34", "#ba3927", "#872517",
                "#f5baba", "#b88c8c", "#8c6f6f")

plot_bw_profile(flist, labels = labels, colors = color_list, loci = court_genes, upstream = 5000, downstream = 5000, mode = "stretch")  + theme_default(base_size = 12) + theme(legend.position = c(0.80, 0.75)) + labs(x = "Court Bivalent 2017")


sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=sv_SE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=sv_SE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=sv_SE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] svglite_2.0.0        corrplot_0.90        heatmaply_1.2.1     
 [4] viridis_0.6.1        viridisLite_0.4.0    plotly_4.9.4.1      
 [7] wigglescout_0.13.1   cowplot_1.1.1        ggrastr_0.2.3       
[10] ggpubr_0.4.0         effsize_0.8.1        forcats_0.5.1       
[13] stringr_1.4.0        dplyr_1.0.7          purrr_0.3.4         
[16] readr_1.4.0          tidyr_1.1.3          tibble_3.1.4        
[19] ggplot2_3.3.5        tidyverse_1.3.1      rtracklayer_1.52.0  
[22] GenomicRanges_1.44.0 GenomeInfoDb_1.28.1  IRanges_2.26.0      
[25] S4Vectors_0.30.0     BiocGenerics_0.38.0  workflowr_1.6.2     

loaded via a namespace (and not attached):
  [1] readxl_1.3.1                backports_1.2.1            
  [3] systemfonts_1.0.2           plyr_1.8.6                 
  [5] lazyeval_0.2.2              BiocParallel_1.26.0        
  [7] listenv_0.8.0               digest_0.6.27              
  [9] foreach_1.5.1               htmltools_0.5.2            
 [11] fansi_0.5.0                 magrittr_2.0.1             
 [13] openxlsx_4.2.4              globals_0.14.0             
 [15] Biostrings_2.60.2           modelr_0.1.8               
 [17] matrixStats_0.60.1          colorspace_2.0-2           
 [19] rvest_1.0.0                 haven_2.4.1                
 [21] xfun_0.24                   crayon_1.4.1               
 [23] RCurl_1.98-1.4              jsonlite_1.7.2             
 [25] iterators_1.0.13            glue_1.4.2                 
 [27] registry_0.5-1              gtable_0.3.0               
 [29] zlibbioc_1.38.0             XVector_0.32.0             
 [31] webshot_0.5.2               DelayedArray_0.18.0        
 [33] car_3.0-11                  abind_1.4-5                
 [35] scales_1.1.1                DBI_1.1.1                  
 [37] rstatix_0.7.0               Rcpp_1.0.7                 
 [39] foreign_0.8-81              htmlwidgets_1.5.3          
 [41] httr_1.4.2                  RColorBrewer_1.1-2         
 [43] ellipsis_0.3.2              farver_2.1.0               
 [45] pkgconfig_2.0.3             XML_3.99-0.7               
 [47] sass_0.4.0                  dbplyr_2.1.1               
 [49] utf8_1.2.2                  labeling_0.4.2             
 [51] tidyselect_1.1.1            rlang_0.4.11               
 [53] reshape2_1.4.4              later_1.3.0                
 [55] munsell_0.5.0               cellranger_1.1.0           
 [57] tools_4.1.1                 cli_3.0.1                  
 [59] generics_0.1.0              broom_0.7.8                
 [61] evaluate_0.14               fastmap_1.1.0              
 [63] yaml_2.2.1                  knitr_1.33                 
 [65] fs_1.5.0                    zip_2.2.0                  
 [67] dendextend_1.15.1           future_1.21.0              
 [69] whisker_0.4                 xml2_1.3.2                 
 [71] compiler_4.1.1              rstudioapi_0.13            
 [73] beeswarm_0.4.0              curl_4.3.2                 
 [75] ggsignif_0.6.2              reprex_2.0.0               
 [77] bslib_0.2.5.1               stringi_1.7.4              
 [79] highr_0.9                   lattice_0.20-44            
 [81] Matrix_1.3-4                vctrs_0.3.8                
 [83] pillar_1.6.2                lifecycle_1.0.0            
 [85] furrr_0.2.3                 jquerylib_0.1.4            
 [87] data.table_1.14.0           bitops_1.0-7               
 [89] seriation_1.3.0             httpuv_1.6.2               
 [91] R6_2.5.1                    BiocIO_1.2.0               
 [93] promises_1.2.0.1            TSP_1.1-10                 
 [95] gridExtra_2.3               rio_0.5.27                 
 [97] vipor_0.4.5                 parallelly_1.26.1          
 [99] codetools_0.2-18            assertthat_0.2.1           
[101] SummarizedExperiment_1.22.0 rprojroot_2.0.2            
[103] rjson_0.2.20                withr_2.4.2                
[105] GenomicAlignments_1.28.0    Rsamtools_2.8.0            
[107] GenomeInfoDbData_1.2.6      hms_1.1.0                  
[109] grid_4.1.1                  rmarkdown_2.9              
[111] MatrixGenerics_1.4.0        carData_3.0-4              
[113] git2r_0.28.0                Biobase_2.52.0             
[115] lubridate_1.7.10            ggbeeswarm_0.6.0           
[117] restfulr_0.0.13