Steroidomics: visualization of normalized concentrations

knitr::opts_chunk$set(echo = TRUE, warning=FALSE)

1. Environment Set Up

1.1 Values of RMarkdown parameters

for (i in 1:length(params))
  print(paste('Parameter:', names(params)[i], ' - Value:', params[[i]], '- Class:', class(params[[i]])))
## [1] "Parameter: InputFolder  - Value: ~/DataDir/steroidomics/ - Class: character"

library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(ggplot2)
library(DT)
library(viridis)
## Loading required package: viridisLite

InputFolder <- params$InputFolder

2. Data Upload

Steroidomics <- openxlsx::read.xlsx("./Normalized_Counts_Neuralorganoids_Steroidomics.xlsx")
head(Steroidomics)
##                Sample Timepoint    Sex   Line Condition dht pregnenolone
## 1  1_1CTL04EDay 50CTL     DAY50 Female CTL04E       CTL   0     202.4586
## 2  1_2CTL04EDay 50CTL     DAY50 Female CTL04E       CTL   0     304.2842
## 3  1_3CTL04EDay 50CTL     DAY50 Female CTL04E       CTL   0     172.5682
## 4 1_4CTL04EDay 50DMSO     DAY50 Female CTL04E      DMSO   0     205.2690
## 5 1_5CTL04EDay 50DMSO     DAY50 Female CTL04E      DMSO   0     213.8746
## 6 1_6CTL04EDay 50DMSO     DAY50 Female CTL04E      DMSO   0     359.4976
##   testosterone androstenedione corticosterone cortisol progesterone cortisone
## 1            0               0       527.3886 2.027865            0 1.8435876
## 2            0               0       669.2955 1.187653            0 0.4624972
## 3            0               0       506.3620 1.658182            0 1.3603737
## 4            0               0       402.3395 0.000000            0 0.0000000
## 5            0               0       475.0151 0.000000            0 0.0000000
## 6            0               0       688.0275 0.000000            0 0.0000000
##   DHEA Androsterone Androstanedione E1 17bE2 E3 17aE2
## 1    0            0               0  0     0  0     0
## 2    0            0               0  0     0  0     0
## 3    0            0               0  0     0  0     0
## 4    0            0               0  0     0  0     0
## 5    0            0               0  0     0  0     0
## 6    0            0               0  0     0  0     0

colnames(Steroidomics)

##  [1] "Sample"          "Timepoint"       "Sex"             "Line"           
##  [5] "Condition"       "dht"             "pregnenolone"    "testosterone"   
##  [9] "androstenedione" "corticosterone"  "cortisol"        "progesterone"   
## [13] "cortisone"       "DHEA"            "Androsterone"    "Androstanedione"
## [17] "E1"              "17bE2"           "E3"              "17aE2"

Measured compounds

dht
pregnenolone
testosterone
androstenedione
corticosterone
cortisol
progesterone
corticone
DHEA
Androsterone
Androstanedione
E1
17bE2
E3
17aB2

densPlot <- function(myData, compound){
  
  ggplot(data=myData, aes(x=(!!sym(compound)), group=Line, fill=Line)) +
  geom_density(adjust=1.5, alpha=.4) +
  scale_fill_viridis(discrete=TRUE) +
    theme_minimal() +
    theme(axis.title.y=element_blank())

  }



boxPlot <- function(myData, compound){
  
  ggplot(data=myData, aes(x=(!!sym(compound)), y=Condition, fill=Line)) +
  geom_boxplot(alpha=0.5, size=0.5) +
  scale_fill_viridis(discrete=TRUE) +
    theme_minimal() +
  theme(axis.title.y=element_blank())
  }



logPlot <- function(myData, compound){
  
  ggplot(data=myData, aes(y=log2(!!sym(compound)+0.01), x=Condition, fill=Line)) +
  geom_boxplot(alpha=0.5) +
  scale_fill_viridis(discrete=TRUE) +
    theme_minimal() +
    theme(axis.text.x=element_text(angle = 90), axis.title.x=element_blank(), 
          legend.position="bottom")
  }

3. DHT

Distribution

quantile(Steroidomics$dht, probs=(seq(0,1,by=0.1)))
##       0%      10%      20%      30%      40%      50%      60%      70% 
##   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000 
##      80%      90%     100% 
##   0.0000   0.0000 613.1551

sum(Steroidomics$dht != 0)
## [1] 6

min(Steroidomics[Steroidomics$dht!=0, ]$dht)
## [1] 513.3291

compound = 'dht'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

4. Pregnenolone

Distribution

quantile(Steroidomics$pregnenolone, probs=(seq(0,1,by=0.1)))
##        0%       10%       20%       30%       40%       50%       60%       70% 
##  82.52382 139.19264 167.73287 190.56382 213.87455 232.38030 262.54671 297.49156 
##       80%       90%      100% 
## 338.51416 398.37493 601.95010

sum(Steroidomics$pregnenolone != 0)
## [1] 96

min(Steroidomics[Steroidomics$pregnenolone!=0, ]$pregnenolone)
## [1] 82.52382

compound = 'pregnenolone'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

5. Testosterone

Distribution

quantile(Steroidomics$testosterone, probs=(seq(0,1,by=0.1)))
##          0%         10%         20%         30%         40%         50% 
##    0.000000    0.000000    0.000000    0.000000    0.000000    0.000000 
##         60%         70%         80%         90%        100% 
##    0.000000    0.000000    2.259961   18.583802 2165.672842

sum(Steroidomics$testosterone != 0)
## [1] 26

min(Steroidomics[Steroidomics$testosterone!=0, ]$testosterone)
## [1] 0.557104

compound = 'testosterone'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

6. Androstenedione

Distribution

quantile(Steroidomics$androstenedione, probs=(seq(0,1,by=0.1)))
##         0%        10%        20%        30%        40%        50%        60% 
##   0.000000   0.000000   0.000000   0.000000   0.000000   0.000000   0.000000 
##        70%        80%        90%       100% 
##   0.000000   0.000000   2.192375 526.034008

sum(Steroidomics$androstenedione != 0)
## [1] 18

min(Steroidomics[Steroidomics$androstenedione!=0, ]$androstenedione)
## [1] 0.5588584

compound = 'androstenedione'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

7. Corticosterone

Distribution

quantile(Steroidomics$corticosterone, probs=(seq(0,1,by=0.1)))
##          0%         10%         20%         30%         40%         50% 
##    0.000000    8.489496   18.713579   54.532927  222.327325  374.992163 
##         60%         70%         80%         90%        100% 
##  474.670514  538.354417  623.771657  719.409447 2160.034311

sum(Steroidomics$corticosterone != 0)
## [1] 93

min(Steroidomics[Steroidomics$corticosterone!=0, ]$corticosterone)
## [1] 5.569155

compound = 'corticosterone'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

8. Cortisol

Distribution

quantile(Steroidomics$cortisol, probs=(seq(0,1,by=0.1)))
##        0%       10%       20%       30%       40%       50%       60%       70% 
## 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 
##       80%       90%      100% 
## 0.0000000 0.3164978 7.0978172

sum(Steroidomics$cortisol != 0)
## [1] 10

min(Steroidomics[Steroidomics$cortisol!=0, ]$cortisol)
## [1] 0.6329955

compound = 'cortisol'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

9. Progesterone

Distribution

quantile(Steroidomics$progesterone, probs=(seq(0,1,by=0.1)))
##         0%        10%        20%        30%        40%        50%        60% 
##    0.00000    0.00000    0.00000    0.00000    0.00000    0.00000   12.68861 
##        70%        80%        90%       100% 
##   23.10147   35.13130   67.97748 3146.76338

sum(Steroidomics$progesterone != 0)
## [1] 40

min(Steroidomics[Steroidomics$progesterone!=0, ]$progesterone)
## [1] 12.49231

compound = 'progesterone'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

10. Cortisone

Distribution

quantile(Steroidomics$cortisone, probs=(seq(0,1,by=0.1)))
##        0%       10%       20%       30%       40%       50%       60%       70% 
## 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 
##       80%       90%      100% 
## 0.5683052 0.7540392 2.1997760

sum(Steroidomics$cortisone != 0)
## [1] 28

min(Steroidomics[Steroidomics$cortisone!=0, ]$cortisone)
## [1] 0.3973228

compound = 'cortisone'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

11. DHEA

Distribution

quantile(Steroidomics$DHEA, probs=(seq(0,1,by=0.1)))
##       0%      10%      20%      30%      40%      50%      60%      70% 
##  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000 
##      80%      90%     100% 
##  0.00000  0.00000 36.60423

sum(Steroidomics$DHEA != 0)
## [1] 3

min(Steroidomics[Steroidomics$DHEA!=0, ]$DHEA)
## [1] 24.42334

compound = 'DHEA'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

12. Androsterone

Distribution

quantile(Steroidomics$Androsterone, probs=(seq(0,1,by=0.1)))
##       0%      10%      20%      30%      40%      50%      60%      70% 
##    0.000    0.000    0.000    0.000    0.000    0.000    0.000    0.000 
##      80%      90%     100% 
##    0.000    0.000 2535.061

sum(Steroidomics$Androsterone != 0)
## [1] 6

min(Steroidomics[Steroidomics$Androsterone!=0, ]$Androsterone)
## [1] 723.3259

compound = 'Androsterone'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

13. Androstanedione

Distribution

quantile(Steroidomics$Androstanedione, probs=(seq(0,1,by=0.1)))
##       0%      10%      20%      30%      40%      50%      60%      70% 
##    0.000    0.000    0.000    0.000    0.000    0.000    0.000    0.000 
##      80%      90%     100% 
##    0.000    0.000 1047.017

sum(Steroidomics$Androstanedione != 0)
## [1] 3

min(Steroidomics[Steroidomics$Androstanedione!=0, ]$Androstanedione)
## [1] 971.4318

compound = 'Androstanedione'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

14. E1

Distribution

quantile(Steroidomics$E1, probs=(seq(0,1,by=0.1)))
##           0%          10%          20%          30%          40%          50% 
##    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000 
##          60%          70%          80%          90%         100% 
##    0.3759819    0.6547111    1.8515653   46.4405075 3430.6624806

sum(Steroidomics$E1 != 0)
## [1] 46

min(Steroidomics[Steroidomics$E1!=0, ]$Androstanedione)
## [1] 0

compound = 'E1'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

15. E3

Distribution

quantile(Steroidomics$E3, probs=(seq(0,1,by=0.1)))
##      0%     10%     20%     30%     40%     50%     60%     70%     80%     90% 
## 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 
##    100% 
## 1.00914

sum(Steroidomics$E3 != 0)
## [1] 6

min(Steroidomics[Steroidomics$E3!=0, ]$Androstanedione)
## [1] 0

compound = 'E3'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

16. 17aE2

Distribution

quantile(Steroidomics$`17aE2`, probs=(seq(0,1,by=0.1)))
##           0%          10%          20%          30%          40%          50% 
##    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000 
##          60%          70%          80%          90%         100% 
##    0.0000000    0.0000000    0.4177229    8.6347623 1859.3658774

sum(Steroidomics$`17aE2` != 0)
## [1] 20

min(Steroidomics[Steroidomics$`17aE2`!=0, ]$`17aE2`)
## [1] 0.4177229

compound = '17aE2'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

17. 17bE2

Distribution

quantile(Steroidomics$`17bE2`, probs=(seq(0,1,by=0.1)))
##          0%         10%         20%         30%         40%         50% 
##    0.000000    0.000000    0.000000    0.000000    0.000000    0.000000 
##         60%         70%         80%         90%        100% 
##    0.000000    0.492749    2.539585  101.072799 5231.595390

sum(Steroidomics$`17bE2` != 0)
## [1] 31

min(Steroidomics[Steroidomics$`17bE2`!=0, ]$`17bE2`)
## [1] 0.490462

compound = '17bE2'
densPlot(Steroidomics, compound)

Boxplot

boxPlot(Steroidomics, compound)

Log Boxplot

logPlot(Steroidomics, compound)

18. SessionInfo

SessionInfo <- sessionInfo()
Date <- date()

Date

## [1] "Wed Aug 13 12:57:38 2025"

SessionInfo

## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] viridis_0.6.2     viridisLite_0.4.1 DT_0.27           ggplot2_3.4.1    
## [5] dplyr_1.1.0      
## 
## loaded via a namespace (and not attached):
##  [1] zip_2.2.2         Rcpp_1.0.10       highr_0.10        pillar_1.8.1     
##  [5] bslib_0.4.2       compiler_4.2.1    jquerylib_0.1.4   tools_4.2.1      
##  [9] digest_0.6.31     jsonlite_1.8.4    evaluate_0.20     lifecycle_1.0.3  
## [13] tibble_3.2.1      gtable_0.3.1      pkgconfig_2.0.3   rlang_1.1.1      
## [17] openxlsx_4.2.5.2  cli_3.6.1         rstudioapi_0.14   yaml_2.3.7       
## [21] xfun_0.37         fastmap_1.1.1     gridExtra_2.3     withr_2.5.0      
## [25] knitr_1.42        generics_0.1.3    vctrs_0.6.2       sass_0.4.5       
## [29] htmlwidgets_1.6.1 grid_4.2.1        tidyselect_1.2.0  glue_1.6.2       
## [33] R6_2.5.1          fansi_1.0.4       rmarkdown_2.20    farver_2.1.1     
## [37] magrittr_2.0.3    scales_1.2.1      htmltools_0.5.4   colorspace_2.1-0 
## [41] labeling_0.4.2    utf8_1.2.3        stringi_1.7.12    munsell_0.5.0    
## [45] cachem_1.0.7

Steroidomics: visualization of normalized concentrations

Date: August 13, 2025

1. Environment Set Up

1.1 Values of RMarkdown parameters

2. Data Upload

3. DHT

Distribution

Boxplot

Log Boxplot

4. Pregnenolone

Distribution

Boxplot

Log Boxplot

5. Testosterone

Distribution

Boxplot

Log Boxplot

6. Androstenedione

Distribution

Boxplot

Log Boxplot

7. Corticosterone

Distribution

Boxplot

Log Boxplot

8. Cortisol

Distribution

Boxplot

Log Boxplot

9. Progesterone

Distribution

Boxplot

Log Boxplot

10. Cortisone

Distribution

Boxplot

Log Boxplot

11. DHEA

Distribution

Boxplot

Log Boxplot

12. Androsterone

Distribution

Boxplot

Log Boxplot

13. Androstanedione

Distribution

Boxplot

Log Boxplot

14. E1

Distribution

Boxplot

Log Boxplot

15. E3

Distribution

Boxplot

Log Boxplot

16. 17aE2

Distribution

Boxplot

Log Boxplot

17. 17bE2

Distribution

Boxplot

Log Boxplot

18. SessionInfo