Last updated: 2024-06-10

Checks: 7 0

Knit directory: PPP/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .RData
    Ignored:    .Rhistory
    Ignored:    code/.DS_Store
    Ignored:    code/TieDIE-devel/.DS_Store
    Ignored:    code/TieDIE-devel/examples/.DS_Store
    Ignored:    code/TieDIE-devel/examples/hnsc/.DS_Store
    Ignored:    code/TieDIE-tiedie2/.DS_Store
    Ignored:    code/TieDIE-tiedie2/examples/.DS_Store
    Ignored:    data/.DS_Store
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    Ignored:    data/Proteome_BCM_GENCODE_v34_harmonized_v1/README/.DS_Store
    Ignored:    output/.DS_Store
    Ignored:    output/cnv/.DS_Store
    Ignored:    output/phos_processed/
    Ignored:    output/phos_regul_object/
    Ignored:    output/regulon/.DS_Store

Untracked files:
    Untracked:  analysis/smVIPER_1.Rmd

Unstaged changes:
    Modified:   analysis/index.Rmd
    Modified:   code/TieDIE-devel/examples/hnsc/Makefile
    Modified:   code/TieDIE-devel/examples/hnsc/exprs.txt
    Modified:   code/TieDIE-devel/examples/hnsc/methy.txt
    Modified:   code/TieDIE-devel/examples/hnsc/pathway.sif
    Modified:   code/TieDIE-devel/examples/hnsc/phos.txt
    Modified:   code/TieDIE-devel/examples/hnsc/prot.txt
    Modified:   code/TieDIE-devel/examples/kirc/CNV.txt
    Modified:   code/TieDIE-devel/examples/kirc/Makefile
    Modified:   code/TieDIE-devel/examples/kirc/exprs.txt
    Modified:   code/TieDIE-devel/examples/kirc/methy.txt
    Modified:   code/TieDIE-devel/examples/kirc/pathway.sif
    Modified:   code/TieDIE-devel/examples/kirc/phos.txt
    Modified:   code/TieDIE-devel/examples/kirc/prot.txt
    Modified:   code/TieDIE-devel/examples/luad/CNV.txt
    Modified:   code/TieDIE-devel/examples/luad/Makefile
    Modified:   code/TieDIE-devel/examples/luad/methy.txt
    Modified:   code/TieDIE-devel/examples/luad/pathway.sif
    Modified:   code/TieDIE-devel/examples/luad/phos.txt
    Modified:   code/TieDIE-devel/examples/luad/prot.txt
    Modified:   code/TieDIE-devel/examples/lusc/Makefile
    Modified:   code/TieDIE-devel/examples/lusc/exprs.txt
    Modified:   code/TieDIE-devel/examples/lusc/methy.txt
    Modified:   code/TieDIE-devel/examples/lusc/pathway.sif
    Modified:   code/TieDIE-devel/examples/lusc/phos.txt
    Modified:   code/TieDIE-devel/examples/lusc/prot.txt
    Modified:   code/TieDIE-devel/examples/paad/CNV.txt
    Modified:   code/TieDIE-devel/examples/paad/Makefile
    Modified:   code/TieDIE-devel/examples/paad/exprs.txt
    Modified:   code/TieDIE-devel/examples/paad/methy.txt
    Modified:   code/TieDIE-devel/examples/paad/pathway.sif
    Modified:   code/TieDIE-devel/examples/paad/phos.txt
    Modified:   code/TieDIE-devel/examples/paad/prot.txt

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TieDIE Results

library(igraph)

Attaching package: 'igraph'
The following objects are masked from 'package:stats':

    decompose, spectrum
The following object is masked from 'package:base':

    union
library(networkD3)
knitr::opts_chunk$set(fig.width=10, fig.height=10)

HNSC

sif_data <- read.table("code/TieDIE-devel/examples/hnsc/TieDIE/TieDIE.sif", header = FALSE, stringsAsFactors = FALSE)
p <- simpleNetwork(sif_data[1:100,c("V1","V3")], height="100px", width="100px",        
        Source = 1,                 # column number of source
        Target = 2,                 # column number of target
        linkDistance = 10,          # distance between node. Increase this value to have more space between nodes
        charge = -900,                # numeric value indicating either the strength of the node repulsion (negative value) or attraction (positive value)
        fontSize = 14,               # size of the node names
        fontFamily = "serif",       # font og node names
        linkColour = "#666",        # colour of edges, MUST be a common colour for the whole graph
        nodeColour = "#69b3a2",     # colour of nodes, MUST be a common colour for the whole graph
        opacity = 0.9,              # opacity of nodes. 0=transparent. 1=no transparency
        zoom = T                    # Can you zoom on the figure?
        )
p

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] networkD3_0.4   igraph_2.0.3    workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8    compiler_4.4.0    promises_1.3.0    Rcpp_1.0.12      
 [5] stringr_1.5.1     git2r_0.33.0      callr_3.7.6       later_1.3.2      
 [9] jquerylib_0.1.4   yaml_2.3.8        fastmap_1.2.0     R6_2.5.1         
[13] knitr_1.46        htmlwidgets_1.6.4 tibble_3.2.1      rprojroot_2.0.4  
[17] bslib_0.7.0       pillar_1.9.0      rlang_1.1.3       utf8_1.2.4       
[21] cachem_1.1.0      stringi_1.8.4     httpuv_1.6.15     xfun_0.44        
[25] getPass_0.2-4     fs_1.6.4          sass_0.4.9        cli_3.6.2        
[29] magrittr_2.0.3    ps_1.7.6          digest_0.6.35     processx_3.8.4   
[33] rstudioapi_0.16.0 lifecycle_1.0.4   vctrs_0.6.5       evaluate_0.23    
[37] glue_1.7.0        whisker_0.4.1     fansi_1.0.6       rmarkdown_2.27   
[41] httr_1.4.7        tools_4.4.0       pkgconfig_2.0.3   htmltools_0.5.8.1