Last updated: 2021-07-05

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Knit directory: Embryoid_Body_Pilot_Workflowr/analysis/

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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/Pseudobulk_HierarchicalClustering_Harmony.Batchindividual_ClusterRes0.5_minPCT0.2.Rmd) and HTML (docs/Pseudobulk_HierarchicalClustering_Harmony.Batchindividual_ClusterRes0.5_minPCT0.2.html) files. If you've configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html 4e5b964 KLRhodes 2020-08-31 Build site.
Rmd 1bd899e KLRhodes 2020-08-31 wflow_publish("analysis/Pseudobulk_HierarchicalClustering_Harmony.Batchindividual_ClusterRes*") 
library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.7.4
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
library(edgeR)
Loading required package: limma
f<- 'Harmony.Batchindividual'
pct<-0.2
res<- 'SCT_snn_res.0.5'
path<- here::here("output/DGELists/")
dge<- readRDS(paste0(path,"Pseudobulk_dge_",f, "_", res,"_minPCT",pct,".rds"))
pseudo.lcpm<- cpm(dge, log=TRUE)
ha<- HeatmapAnnotation(cluster= dge$samples$cluster, batch= dge$samples$batch, individual= dge$samples$ind)

Heatmap(pseudo.lcpm, bottom_annotation = ha, show_column_names = F, show_row_names = F, name = "lcpm", use_raster = TRUE)

Version Author Date
4e5b964 KLRhodes 2020-08-31

Same thing, removing ribosomal to see if it changes anything

genes.ribo <- grep('^RP',rownames(dge),value=T)
genes.no.ribo <- rownames(dge)[which(!(rownames(dge) %in% genes.ribo))]
dge$counts <- dge$counts[which(rownames(dge$counts) %in% genes.no.ribo),] #remove ribosomal genes
pseudo.lcpm<- cpm(dge, log=TRUE)
ha<- HeatmapAnnotation(cluster= dge$samples$cluster, batch= dge$samples$batch, individual= dge$samples$ind)

Heatmap(pseudo.lcpm, bottom_annotation = ha, show_column_names = F, show_row_names = F, name = "lcpm", use_raster = TRUE)

Version Author Date
4e5b964 KLRhodes 2020-08-31 
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
[1] C

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

other attached packages:
[1] edgeR_3.28.1         limma_3.42.2         ComplexHeatmap_2.7.4
[4] workflowr_1.6.2     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6          RColorBrewer_1.1-2  pillar_1.4.7       
 [4] compiler_3.6.1      later_1.1.0.1       git2r_0.26.1       
 [7] tools_3.6.1         digest_0.6.27       lattice_0.20-38    
[10] clue_0.3-58         evaluate_0.14       lifecycle_0.2.0    
[13] tibble_3.0.4        pkgconfig_2.0.3     png_0.1-7          
[16] rlang_0.4.10        magick_2.4.0        yaml_2.2.1         
[19] parallel_3.6.1      xfun_0.16           cluster_2.1.0      
[22] stringr_1.4.0       knitr_1.29          S4Vectors_0.24.4   
[25] fs_1.4.2            vctrs_0.3.6         GlobalOptions_0.1.2
[28] IRanges_2.20.2      locfit_1.5-9.4      stats4_3.6.1       
[31] rprojroot_2.0.2     here_0.1-11         glue_1.4.2         
[34] R6_2.5.0            GetoptLong_1.0.5    rmarkdown_2.3      
[37] magrittr_2.0.1      whisker_0.4         promises_1.1.1     
[40] ellipsis_0.3.1      htmltools_0.5.0     matrixStats_0.57.0 
[43] BiocGenerics_0.32.0 shape_1.4.5         colorspace_2.0-0   
[46] circlize_0.4.11     httpuv_1.5.4        stringi_1.5.3      
[49] crayon_1.3.4        rjson_0.2.20        Cairo_1.5-12.2     

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
[1] C

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

other attached packages:
[1] edgeR_3.28.1         limma_3.42.2         ComplexHeatmap_2.7.4
[4] workflowr_1.6.2     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6          RColorBrewer_1.1-2  pillar_1.4.7       
 [4] compiler_3.6.1      later_1.1.0.1       git2r_0.26.1       
 [7] tools_3.6.1         digest_0.6.27       lattice_0.20-38    
[10] clue_0.3-58         evaluate_0.14       lifecycle_0.2.0    
[13] tibble_3.0.4        pkgconfig_2.0.3     png_0.1-7          
[16] rlang_0.4.10        magick_2.4.0        yaml_2.2.1         
[19] parallel_3.6.1      xfun_0.16           cluster_2.1.0      
[22] stringr_1.4.0       knitr_1.29          S4Vectors_0.24.4   
[25] fs_1.4.2            vctrs_0.3.6         GlobalOptions_0.1.2
[28] IRanges_2.20.2      locfit_1.5-9.4      stats4_3.6.1       
[31] rprojroot_2.0.2     here_0.1-11         glue_1.4.2         
[34] R6_2.5.0            GetoptLong_1.0.5    rmarkdown_2.3      
[37] magrittr_2.0.1      whisker_0.4         promises_1.1.1     
[40] ellipsis_0.3.1      htmltools_0.5.0     matrixStats_0.57.0 
[43] BiocGenerics_0.32.0 shape_1.4.5         colorspace_2.0-0   
[46] circlize_0.4.11     httpuv_1.5.4        stringi_1.5.3      
[49] crayon_1.3.4        rjson_0.2.20        Cairo_1.5-12.2