Last updated: 2021-08-16
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Knit directory: Turati_NatCancer_2021/
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| Rmd | 73647b7 | Javier Herrero | 2021-08-13 | Adding the “Data / Ancillary” page |
| html | 73647b7 | Javier Herrero | 2021-08-13 | Adding the “Data / Ancillary” page |
| Rmd | 3b68b3c | Javier Herrero | 2021-08-13 | Adding data / Bulk RNAseq page |
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library(tidyverse)
library(DT)This table show the number of datasets per sample per patient. The numbers correspond to the number of cells or samples after QC.
samples_summary <- read_csv("data-raw/samples_summary.csv", col_types = "cccc")
samples_summary %>%
pivot_wider(names_from = "Assay", values_from = n_samples, values_fill = list(n_samples = "")) %>%
select(Patient, Sample, `Bulk RNA`, scRNA, scWGS, EPIC, `Bulk WGS`, `sc Q-PCR`) %>%
cbind(prev_patient = c("", .$Patient[1:(nrow(.)-1)])) %>%
mutate(Patient = ifelse(Patient == prev_patient, "", Patient)) %>%
select(-prev_patient) %>%
datatable(rownames = F, options = list(pageLength = 100, ordering = F, dom = 't')) %>%
formatStyle(c('Patient', 'Sample'), fontWeight = "bold") %>%
formatStyle(2:8, 'Sample', backgroundColor =
styleEqual(c("Diagnosis", "MRD (G&T)", "Relapse",
"PDX untreated", "PDX treated", "PDX withdrawn",
"PDX chronically", "PDX acutely", "PDX relapse",
"chord blood"),
c("#FCE4D6", "#FCE4D6", "#FCE4D6",
"#DDEBF7", "#DDEBF7", "#DDEBF7",
"#DDEBF7", "#DDEBF7", "#DDEBF7",
"#E2EFDA"))) %>%
formatStyle(3:8, backgroundColor = styleEqual("", "#D9D9D9")) %>%
formatStyle(1:8, borderColor = "black") %>%
formatStyle(1:8, "Patient", borderColor = styleEqual("", "#CCCCCC")) %>%
formatStyle(1, borderLeft = "solid 1px") %>%
formatStyle(c(1, 2, 8), borderRight = "solid 1px") %>%
formatStyle(c(3:7), borderRight = "solid 1px #CCCCCC")Preprocessing of the bulk RNA-seq data
Under construction
Under construction
Gene sets and color palette.
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.13 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0
[5] purrr_0.3.3 readr_1.3.1 tidyr_1.0.2 tibble_2.1.3
[9] ggplot2_3.3.1 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.16 haven_2.2.0 lattice_0.20-40
[5] colorspace_1.4-1 vctrs_0.3.0 generics_0.0.2 htmltools_0.5.1.1
[9] yaml_2.2.1 base64enc_0.1-3 rlang_0.4.11 later_1.0.0
[13] pillar_1.4.3 withr_2.4.2 glue_1.3.2 DBI_1.1.0
[17] dbplyr_1.4.2 modelr_0.1.6 readxl_1.3.1 lifecycle_0.2.0
[21] munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_0.3.5
[25] htmlwidgets_1.5.1 evaluate_0.14 knitr_1.28 crosstalk_1.1.0.1
[29] httpuv_1.5.2 broom_0.5.5 Rcpp_1.0.4 promises_1.1.0
[33] backports_1.1.5 scales_1.1.0 jsonlite_1.6.1 fs_1.3.2
[37] hms_0.5.3 digest_0.6.25 stringi_1.4.6 grid_3.6.3
[41] rprojroot_1.3-2 cli_3.0.0 tools_3.6.3 magrittr_1.5
[45] crayon_1.3.4 whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.0
[49] xml2_1.2.5 reprex_0.3.0 lubridate_1.7.4 rstudioapi_0.11
[53] assertthat_0.2.1 rmarkdown_2.1 httr_1.4.1 R6_2.4.1
[57] nlme_3.1-145 git2r_0.26.1 compiler_3.6.3