Last updated: 2021-07-28

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Knit directory: Multispectral HCC/

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File Version Author Date Message
Rmd c4324f5 Jovan Tanevski 2021-07-28 add umap
html 0bfae68 Jovan Tanevski 2021-07-28 Build site.
Rmd 82e3712 Jovan Tanevski 2021-07-28 add basic hclust

Setup

Load required libraries.

library(tidyverse)
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✓ ggplot2 3.3.5     ✓ purrr   0.3.4
✓ tibble  3.1.3     ✓ dplyr   1.0.7
✓ tidyr   1.1.3     ✓ stringr 1.4.0
✓ readr   2.0.0     ✓ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
library(skimr)
library(uwot)
Loading required package: Matrix

Attaching package: 'Matrix'
The following objects are masked from 'package:tidyr':

    expand, pack, unpack

Read filtered TCGA RRPA data and display summary statistics.

tcga <- read_csv("data/TCGA-RPPA-LIHC_selected.csv", col_types = cols())
skim(tcga)
Data summary
Name tcga
Number of rows 184
Number of columns 14
_______________________
Column type frequency:
character 2
numeric 12
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
SampleID 0 1 27 27 0 184 0
TumorType 0 1 4 4 0 1 0

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
P53 0 1 -1.13 0.46 -2.54 -1.40 -0.96 -0.76 -0.51 ▁▂▂▅▇
AKT_pS473 0 1 -0.63 0.71 -2.76 -1.02 -0.41 -0.15 0.96 ▁▂▃▇▁
AKT_pT308 0 1 0.07 0.42 -1.16 -0.07 0.09 0.22 1.72 ▁▃▇▁▁
BETACATENIN 0 1 1.50 0.72 -1.30 1.08 1.51 1.87 3.70 ▁▁▇▅▁
JNK_pT183Y185 0 1 -0.21 0.29 -1.14 -0.36 -0.17 -0.04 0.48 ▁▂▇▇▂
MEK1_pS217S221 0 1 -0.17 0.36 -0.82 -0.35 -0.23 -0.10 2.58 ▇▃▁▁▁
P38_pT180Y182 0 1 0.49 0.57 -1.45 0.31 0.50 0.72 2.95 ▁▂▇▁▁
P70S6K_pT389 0 1 -1.21 0.75 -3.22 -1.58 -0.95 -0.65 1.09 ▂▃▇▃▁
PDK1_pS241 0 1 0.40 0.31 -0.56 0.23 0.37 0.55 1.62 ▁▇▇▂▁
S6_pS235S236 0 1 -0.72 0.75 -3.53 -1.06 -0.67 -0.36 1.12 ▁▁▅▇▂
YAP_pS127 0 1 2.21 0.61 0.68 1.78 2.10 2.54 4.05 ▁▇▇▂▁
TRANSGLUTAMINASE 0 1 -0.42 0.56 -1.24 -0.83 -0.59 -0.20 2.72 ▇▃▁▁▁

Unsupervised analysis

Perform hierarchical clustering of the data and plot the resulting dendrogram

tcga.dist <- dist(tcga %>% select(-SampleID, -TumorType))
tcga.hclust <- hclust(tcga.dist, method = "average")

plot(tcga.hclust,
  hang = -1, cex = 0.6,
  labels = tcga %>% pull("SampleID") %>%
    str_extract("[A-Z0-9]{2}-[A-Z0-9]{4}")
)

Version Author Date
0bfae68 Jovan Tanevski 2021-07-28

Project to 2D with UMAP and plot

tcga.umap <- umap(tcga %>% select(-SampleID, -TumorType),
  n_neighbors = 5, n_epochs = 1000
)
colnames(tcga.umap) <- c("U1", "U2")

ggplot(tcga.umap %>% as_tibble(), aes(x = U1, y = U2)) +
  geom_point() +
  theme_classic()


sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] uwot_0.1.10     Matrix_1.3-4    skimr_2.1.3     forcats_0.5.1  
 [5] stringr_1.4.0   dplyr_1.0.7     purrr_0.3.4     readr_2.0.0    
 [9] tidyr_1.1.3     tibble_3.1.3    ggplot2_3.3.5   tidyverse_1.3.1
[13] workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] httr_1.4.2        sass_0.4.0        bit64_4.0.5       vroom_1.5.3      
 [5] jsonlite_1.7.2    modelr_0.1.8      bslib_0.2.5.1     assertthat_0.2.1 
 [9] highr_0.9         cellranger_1.1.0  yaml_2.2.1        pillar_1.6.1     
[13] backports_1.2.1   lattice_0.20-44   glue_1.4.2        digest_0.6.27    
[17] promises_1.2.0.1  rvest_1.0.0       colorspace_2.0-2  htmltools_0.5.1.1
[21] httpuv_1.6.1      pkgconfig_2.0.3   broom_0.7.8       haven_2.4.1      
[25] scales_1.1.1      whisker_0.4       RSpectra_0.16-0   later_1.2.0      
[29] tzdb_0.1.2        git2r_0.28.0      generics_0.1.0    farver_2.1.0     
[33] ellipsis_0.3.2    withr_2.4.2       repr_1.1.3        cli_3.0.1        
[37] magrittr_2.0.1    crayon_1.4.1      readxl_1.3.1      evaluate_0.14    
[41] fs_1.5.0          fansi_0.5.0       xml2_1.3.2        FNN_1.1.3        
[45] tools_4.1.0       hms_1.1.0         lifecycle_1.0.0   munsell_0.5.0    
[49] reprex_2.0.0      compiler_4.1.0    jquerylib_0.1.4   rlang_0.4.11     
[53] grid_4.1.0        rstudioapi_0.13   base64enc_0.1-3   labeling_0.4.2   
[57] rmarkdown_2.9     gtable_0.3.0      DBI_1.1.1         R6_2.5.0         
[61] lubridate_1.7.10  knitr_1.33        bit_4.0.4         utf8_1.2.2       
[65] rprojroot_2.0.2   stringi_1.7.3     parallel_4.1.0    Rcpp_1.0.7       
[69] vctrs_0.3.8       dbplyr_2.1.1      tidyselect_1.1.1  xfun_0.24