Chapter 27 Writing files to file
Update the metadata file: write to file:
- updated ext data table
- spatial information summary
- star aligned table
- colData information
- collapsed information on wsi/facs
write.xlsx(Cdata, file=sprintf("../metadata/Ext_Data_Table_updated_%s.xlsx", Sys.Date()))
#colnames(Cdata)
x1=match(rownames(df.Spatial), gsub("_","", Cdata$TumorID))
df.Spatial$NewID=Cdata$NewID[x1]
dfB=Cdata[x1, c("NewID", "TumorID","TumorAreaWSI", "Tumor.diameter.sac.mm", "CD45.Frac.FACS",
"DN.Frac.FACS", "EpCAM.Frac.FACS")]
write.csv(df.Spatial, file="nature-tables/summary_spatial_information.csv")
colnames(allstarFinal)=infoTableFinal$TumorIDnew[match(colnames(allstarFinal), rownames(infoTableFinal))]
infoTableFinal2=infoTableFinal[ ,c("TumorIDnew","Growth", "CD8Frac", "TumSize", "Time.NMU2Sac",
"Age.Injection","Treatment","Cohort", "SizeCat")]
write.csv(infoTableFinal2, file="nature-tables/infoTableFinal2_output.csv")
write.csv(allstarFinal, file="nature-tables/allstarFinal_output.csv")
colTestCD8=c("CD8.EpBoundingBox", "CD8.TumSize", "CD45.FACS", "CD8.FACS", "OverallCD8_Fig4c.Manual", "TIL_Fig4d.Manual", "T.cell.CD8._TIMER", "T.cell.CD8._CIBERSORT","T.cell.CD8._CIBERSORT.ABS", "T.cell.CD8._EPIC")
# colTestCD8=c("CD8.EpDomTiles","CD8.EpBoundingBox", "CD8.TumSize", "CD45.FACS", "CD8.FACS", "OverallCD8_Fig4c.Manual", "TIL_Fig4d.Manual", )
indx1=c("CD8.WSI", "CD8Frac.WSI", "CD8_EPorSMARatio.WSI","CD8_AnyEPRatio.WSI", "CD8_EPRatio.WSI","CD8normTumSize", "CD8.EpBoundingBox")
df.Spatial2=merge(df.Spatial, dfB, by.x="NewID", by.y="NewID", all=T)
#head(df.Spatial2)
colnames(ProgSpecCD45)=gsub("_CD45", "", colnames(ProgSpecCD45))
#colnames(ProgSpecCD45)=gsub("_", "", colnames(ProgSpecCD45))
rownames(ProgSpecCD45)=ProgSpecCD45[ ,1]
ProgSpecCD45B=t(ProgSpecCD45[grep("CD8",rownames(ProgSpecCD45)), -1 ])
ProgSpecCD45B=data.frame(ProgSpecCD45B, sample=rownames(ProgSpecCD45B))
df.Spatial3=merge(df.Spatial2, ProgSpecCD45B, by.x="TumorID", by.y="sample", all=T)
df.Spatial3$TumorID2=gsub("_", "", df.Spatial3$TumorID)
SummaryData$TumorID2=rownames(SummaryData)
df.Spatial4=merge(df.Spatial3, SummaryData[ ,c(6:8,17:19, ncol(SummaryData))], by.x="TumorID2", by.y="TumorID2", all=T)
write.csv(df.Spatial4, file="../metadata/summary_new_210330.csv")
## merge he data from df.Spatial with the data from
#df1=data.frame(CD8.WSI=df.Spatial$)
# df2=data.frame(CD8.WSI=t(WSIvals[ 1, ]),
# CD8Frac.WSI=t(WSIvalFracs[ ,2]),
# CD8_EPorSMARatio.WSI=(WSIvals[1, ]/colSums(WSIvals[2:4, ])),
# CD8_AnyEPRatio.WSI=(WSIvals[1, ]/colSums(WSIvals[2:3, ])),
# CD8_EPRatio.WSI=(WSIvals[1, ]/(WSIvals[2, ])),
# CD8normTumSize=(WSIvals[1, ]/df.Spatial))
# # )Below is the session info
sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] writexl_1.3.1 xlsx_0.6.4.2
## [3] vcfR_1.12.0 tcR_2.3.2
## [5] igraph_1.2.6 gridExtra_2.3
## [7] spatstat_1.64-1 rpart_4.1-15
## [9] nlme_3.1-149 spatstat.data_1.4-3
## [11] scales_1.1.1 RColorBrewer_1.1-2
## [13] rmarkdown_2.6 reshape2_1.4.4
## [15] pamr_1.56.1 survival_3.2-7
## [17] cluster_2.1.0 limma_3.44.3
## [19] knitr_1.31 kableExtra_1.2.1
## [21] HTSanalyzeR2_0.99.19 heatmap.plus_1.3
## [23] GSVA_1.36.3 GSEABase_1.50.1
## [25] graph_1.66.0 annotate_1.66.0
## [27] XML_3.99-0.5 gplots_3.1.0
## [29] ggrepel_0.8.2 ggplot2_3.3.2
## [31] GenVisR_1.20.0 forestplot_1.10.1
## [33] checkmate_2.0.0 magrittr_1.5
## [35] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.12.1
## [37] AnnotationFilter_1.12.0 GenomicFeatures_1.40.1
## [39] AnnotationDbi_1.50.3 DT_0.17
## [41] dplyr_1.0.2 DESeq2_1.28.1
## [43] SummarizedExperiment_1.18.2 DelayedArray_0.14.1
## [45] matrixStats_0.57.0 Biobase_2.48.0
## [47] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
## [49] colorspace_1.4-1 Biostrings_2.56.0
## [51] XVector_0.28.0 IRanges_2.22.2
## [53] S4Vectors_0.26.1 biomaRt_2.44.4
## [55] beeswarm_0.2.3 AnnotationHub_2.20.2
## [57] BiocFileCache_1.12.1 dbplyr_1.4.4
## [59] BiocGenerics_0.34.0
##
## loaded via a namespace (and not attached):
## [1] shinydashboard_0.7.1 tidyselect_1.1.0
## [3] RSQLite_2.2.1 htmlwidgets_1.5.2
## [5] BiocParallel_1.22.0 gmp_0.6-1
## [7] munsell_0.5.0 codetools_0.2-16
## [9] preprocessCore_1.50.0 miniUI_0.1.1.1
## [11] withr_2.3.0 Category_2.54.0
## [13] highr_0.8 rstudioapi_0.11
## [15] robustbase_0.93-6 splots_1.54.0
## [17] tensor_1.5 rJava_0.9-13
## [19] labeling_0.4.2 GenomeInfoDbData_1.2.3
## [21] polyclip_1.10-0 hwriter_1.3.2
## [23] farver_2.0.3 bit64_4.0.5
## [25] vctrs_0.3.4 generics_0.0.2
## [27] xfun_0.21 R6_2.4.1
## [29] locfit_1.5-9.4 msigdbr_7.2.1
## [31] spatstat.utils_1.17-0 bitops_1.0-6
## [33] fgsea_1.14.0 assertthat_0.2.1
## [35] promises_1.1.1 pinfsc50_1.2.0
## [37] gtable_0.3.0 affy_1.66.0
## [39] goftest_1.2-2 cellHTS2_2.52.0
## [41] rlang_0.4.8 genefilter_1.70.0
## [43] splines_4.0.2 rtracklayer_1.48.0
## [45] lazyeval_0.2.2 abind_1.4-5
## [47] BiocManager_1.30.10 yaml_2.2.1
## [49] crosstalk_1.1.0.1 backports_1.1.10
## [51] httpuv_1.5.4 RBGL_1.64.0
## [53] tools_4.0.2 bookdown_0.21
## [55] affyio_1.58.0 ellipsis_0.3.1
## [57] Rcpp_1.0.5 plyr_1.8.6
## [59] progress_1.2.2 zlibbioc_1.34.0
## [61] purrr_0.3.4 RCurl_1.98-1.2
## [63] prettyunits_1.1.1 deldir_0.1-29
## [65] openssl_1.4.3 viridis_0.5.1
## [67] data.table_1.13.2 colourpicker_1.1.0
## [69] mvtnorm_1.1-1 ProtGenerics_1.20.0
## [71] xlsxjars_0.6.1 hms_0.5.3
## [73] mime_0.9 evaluate_0.14
## [75] xtable_1.8-4 compiler_4.0.2
## [77] tibble_3.0.4 KernSmooth_2.23-17
## [79] crayon_1.3.4 htmltools_0.5.0
## [81] mgcv_1.8-33 pcaPP_1.9-73
## [83] later_1.1.0.1 geneplotter_1.66.0
## [85] rrcov_1.5-5 DBI_1.1.0
## [87] MASS_7.3-53 rappdirs_0.3.1
## [89] Matrix_1.2-18 permute_0.9-5
## [91] vsn_3.56.0 RankProd_3.14.0
## [93] pkgconfig_2.0.3 GenomicAlignments_1.24.0
## [95] xml2_1.3.2 foreach_1.5.1
## [97] prada_1.63.0 stringdist_0.9.6.3
## [99] webshot_0.5.2 rvest_0.3.6
## [101] BioNet_1.47.0 stringr_1.4.0
## [103] VariantAnnotation_1.34.0 digest_0.6.26
## [105] vegan_2.5-6 fastmatch_1.1-0
## [107] curl_4.3 shiny_1.5.0
## [109] Rsamtools_2.4.0 gtools_3.8.2
## [111] FField_0.1.0 jsonlite_1.7.1
## [113] lifecycle_0.2.0 viridisLite_0.3.0
## [115] askpass_1.1 BSgenome_1.56.0
## [117] pillar_1.4.6 lattice_0.20-41
## [119] KEGGREST_1.28.0 fastmap_1.0.1
## [121] httr_1.4.2 DEoptimR_1.0-8
## [123] GO.db_3.11.4 interactiveDisplayBase_1.26.3
## [125] glue_1.4.2 png_0.1-7
## [127] shinythemes_1.1.2 iterators_1.0.13
## [129] BiocVersion_3.11.1 bit_4.0.4
## [131] stringi_1.5.3 blob_1.2.1
## [133] caTools_1.18.0 memoise_1.1.0
## [135] Rmpfr_0.8-1 ape_5.4-1