Last updated: 2021-07-28

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Knit directory: Multispectral HCC/

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File Version Author Date Message
Rmd d0b6e0f Jovan Tanevski 2021-07-28 add pca to tcga analysis
html d73f586 Jovan Tanevski 2021-07-28 Build site.
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
library(factoextra)
Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa

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 PCA and UMAP and plot

tcga.pca <- prcomp(tcga %>% select(-SampleID, -TumorType))
summary(tcga.pca)
Importance of components:
                          PC1    PC2    PC3     PC4     PC5     PC6     PC7
Standard deviation     1.2123 0.8248 0.6607 0.56514 0.52805 0.47568 0.43431
Proportion of Variance 0.3831 0.1773 0.1138 0.08325 0.07268 0.05898 0.04917
Cumulative Proportion  0.3831 0.5604 0.6742 0.75746 0.83014 0.88912 0.93829
                           PC8     PC9   PC10    PC11    PC12
Standard deviation     0.31055 0.24392 0.2216 0.14622 0.10156
Proportion of Variance 0.02514 0.01551 0.0128 0.00557 0.00269
Cumulative Proportion  0.96343 0.97894 0.9917 0.99731 1.00000
fviz_pca_biplot(tcga.pca, label = "var", col.var = "cos2") + theme_classic()

Version Author Date
d73f586 Jovan Tanevski 2021-07-28
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] factoextra_1.0.7 uwot_0.1.10      Matrix_1.3-4     skimr_2.1.3     
 [5] forcats_0.5.1    stringr_1.4.0    dplyr_1.0.7      purrr_0.3.4     
 [9] readr_2.0.0      tidyr_1.1.3      tibble_3.1.3     ggplot2_3.3.5   
[13] tidyverse_1.3.1  workflowr_1.6.2 

loaded via a namespace (and not attached):
 [1] fs_1.5.0          lubridate_1.7.10  bit64_4.0.5       httr_1.4.2       
 [5] rprojroot_2.0.2   repr_1.1.3        tools_4.1.0       backports_1.2.1  
 [9] bslib_0.2.5.1     utf8_1.2.2        R6_2.5.0          DBI_1.1.1        
[13] colorspace_2.0-2  withr_2.4.2       tidyselect_1.1.1  bit_4.0.4        
[17] curl_4.3.2        compiler_4.1.0    git2r_0.28.0      cli_3.0.1        
[21] rvest_1.0.0       xml2_1.3.2        labeling_0.4.2    sass_0.4.0       
[25] scales_1.1.1      digest_0.6.27     foreign_0.8-81    rmarkdown_2.9    
[29] rio_0.5.27        base64enc_0.1-3   pkgconfig_2.0.3   htmltools_0.5.1.1
[33] dbplyr_2.1.1      highr_0.9         rlang_0.4.11      readxl_1.3.1     
[37] rstudioapi_0.13   FNN_1.1.3         farver_2.1.0      jquerylib_0.1.4  
[41] generics_0.1.0    jsonlite_1.7.2    vroom_1.5.3       zip_2.2.0        
[45] car_3.0-11        magrittr_2.0.1    Rcpp_1.0.7        munsell_0.5.0    
[49] fansi_0.5.0       abind_1.4-5       lifecycle_1.0.0   stringi_1.7.3    
[53] whisker_0.4       yaml_2.2.1        carData_3.0-4     grid_4.1.0       
[57] parallel_4.1.0    promises_1.2.0.1  ggrepel_0.9.1     crayon_1.4.1     
[61] lattice_0.20-44   haven_2.4.1       hms_1.1.0         knitr_1.33       
[65] pillar_1.6.1      ggpubr_0.4.0      ggsignif_0.6.2    reprex_2.0.0     
[69] glue_1.4.2        evaluate_0.14     data.table_1.14.0 modelr_0.1.8     
[73] vctrs_0.3.8       tzdb_0.1.2        httpuv_1.6.1      cellranger_1.1.0 
[77] gtable_0.3.0      assertthat_0.2.1  xfun_0.24         openxlsx_4.2.4   
[81] broom_0.7.8       RSpectra_0.16-0   rstatix_0.7.0     later_1.2.0      
[85] ellipsis_0.3.2