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Introduction


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
data <- read.csv("./data/Data_QC_flagged.csv")

  data$Buffer_nl <- as.factor(data$Buffer_nl)


ggplot(data, aes(x = Weight_mg, y = Average_Conc_pg.ml, )) +
  geom_point() +
  geom_smooth(method = "lm", se = FALSE) +  # Add a linear trend line
  labs(title = "Association between Weight and Average Concentration",
       x = "Weight (mg)", y = "Average Concentration (pg/ml)")
`geom_smooth()` using formula = 'y ~ x'

# Scatter plot of Buffer vs Binding Percentage
ggplot(data, aes(x = Buffer_nl, y = Binding.Perc)) +
  geom_boxplot() +
  geom_smooth(method = "lm", se = FALSE) +  # Add a linear trend line
  facet_wrap(data$Spike,scales = "fixed") +
  labs(title = "Association between Buffer and Binding Percentage",
       x = "Buffer (nl)", y = "Binding Percentage") 
`geom_smooth()` using formula = 'y ~ x'

data$Binding_deviation <- abs(data$Binding.Perc - 50)
sorted_data <- data[order(data$Binding_deviation), ]

dim(sorted_data)
[1] 38 14
# View top results (closest to 50% Binding Percentage)
kable(sorted_data)
Sample Wells Raw.OD Binding.Perc Concentration_pg.ml Average_Conc_pg.ml CV.Perc SD SEM Weight_mg Buffer_nl Spike Failed_samples Binding_deviation
26 32 A11 0.656 50.0 1228.0 1197.0 3.690 44.20 31.30 37.1 250 0 NA 0.0
25 31 H9 0.701 51.2 1070.0 1149.0 9.750 112.00 79.20 21.2 60 0 NA 1.2
28 34 C11 0.687 51.7 1117.0 1124.0 0.867 9.74 6.89 35.5 250 0 NA 1.7
27 33 B11 0.696 52.3 1087.0 1100.0 1.730 19.10 13.50 33.8 250 0 NA 2.3
30 36 E11 0.695 53.2 1090.0 1062.0 3.680 39.10 27.60 31.2 250 0 NA 3.2
12 2 D3 0.675 53.8 1159.0 1045.0 15.300 160.00 113.00 17.2 60 0 HIGH CV 3.8
19 27 E9 0.610 46.0 1417.0 1393.0 2.430 33.80 23.90 21.6 60 0 NA 4.0
10 18 D7 0.734 56.0 967.1 955.4 1.740 16.60 11.70 30.8 250 0 NA 6.0
13 20 F7 0.538 43.6 1785.0 1550.0 21.400 332.00 235.00 30.1 60 0 HIGH CV 6.4
20 28 F9 0.757 59.5 901.0 839.7 10.300 86.70 61.30 23.2 250 0 NA 9.5
16 23 A8 0.809 60.9 766.3 793.6 4.880 38.70 27.40 24.6 250 0 NA 10.9
2 10 D5 0.743 37.6 940.7 3064.0 98.000 3000.00 2120.00 17.7 60 1 HIGH CV 12.4
18 26 D9 0.477 37.3 2197.0 1991.0 14.600 291.00 206.00 20.2 60 0 NA 12.7
21 29 G9 0.518 36.2 1907.0 2072.0 11.200 232.00 164.00 36.5 60 0 NA 13.8
31 37 F11 0.482 36.1 2158.0 2076.0 5.620 117.00 82.50 30.8 60 0 NA 13.9
17 24 B9 0.835 64.8 705.5 680.2 5.260 35.80 25.30 20.4 250 0 NA 14.8
35 6 H3 0.490 34.7 2099.0 2204.0 6.750 149.00 105.00 13.7 60 1 NA 15.3
22 3 E3 0.478 33.9 2189.0 2287.0 6.090 139.00 98.50 11.0 60 1 NA 16.1
7 15 A7 0.888 66.2 592.9 643.6 11.100 71.60 50.70 12.0 60 0 NA 16.2
29 35 D11 0.548 33.8 1727.0 2443.0 41.500 1010.00 716.00 32.1 60 0 HIGH CV 16.2
15 22 H7 0.453 33.0 2395.0 2377.0 1.030 24.50 17.40 21.5 250 1 NA 17.0
32 38 G11 0.429 32.5 2619.0 2444.0 10.200 248.00 176.00 34.7 60 0 NA 17.5
5 13 G5 0.451 32.1 2412.0 2477.0 3.680 91.10 64.40 16.8 250 1 NA 17.9
6 14 H5 0.437 31.8 2541.0 2504.0 2.110 52.90 37.40 13.8 250 1 NA 18.2
14 21 G7 0.425 31.6 2660.0 2540.0 6.630 169.00 119.00 28.0 250 1 NA 18.4
36 7 A5 0.436 30.5 2551.0 2669.0 6.250 167.00 118.00 16.4 60 1 NA 19.5
38 9 C5 0.432 30.3 2590.0 2693.0 5.460 147.00 104.00 19.2 250 1 NA 19.7
4 12 F5 0.422 30.0 2690.0 2728.0 1.920 52.50 37.10 24.1 250 1 NA 20.0
23 30A A3 0.403 28.8 2899.0 2888.0 0.565 16.30 11.50 29.6 250 1 NA 21.2
3 11 E5 0.939 71.6 496.8 513.2 4.500 23.10 16.30 17.5 250 0 NA 21.6
34 5 G3 0.944 72.1 488.0 501.4 3.790 19.00 13.40 14.4 60 0 NA 22.1
8 16 B7 0.372 26.8 3297.0 3196.0 4.470 143.00 101.00 23.4 60 1 NA 23.2
11 19 E7 0.364 24.1 3413.0 3730.0 12.000 449.00 317.00 27.9 60 1 NA 25.9
1 1 C3 0.959 77.3 461.9 396.6 23.300 92.40 65.30 13.1 250 0 HIGH CV 27.3
37 8 B5 1.030 77.8 354.9 386.8 11.700 45.10 31.90 15.3 250 0 NA 27.8
33 4 F3 1.070 80.6 295.8 334.5 16.300 54.60 38.60 11.7 250 0 HIGH CV;ABOVE 80% binding 30.6
24 30B B3 1.050 81.1 314.1 324.9 4.700 15.30 10.80 29.6 250 0 ABOVE 80% binding 31.1
9 17 C7 1.080 84.3 278.0 270.6 3.860 10.50 7.39 24.5 60 0 ABOVE 80% binding 34.3 

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.5.1 knitr_1.48    dplyr_1.1.2  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10       highr_0.11        pillar_1.9.0      compiler_4.1.0   
 [5] bslib_0.8.0       later_1.3.0       jquerylib_0.1.4   git2r_0.31.0     
 [9] workflowr_1.7.1   tools_4.1.0       digest_0.6.31     lattice_0.20-44  
[13] nlme_3.1-152      gtable_0.3.5      jsonlite_1.8.4    evaluate_1.0.0   
[17] lifecycle_1.0.4   tibble_3.2.1      mgcv_1.8-35       pkgconfig_2.0.3  
[21] rlang_1.1.0       Matrix_1.3-3      cli_3.6.1         rstudioapi_0.16.0
[25] yaml_2.3.7        xfun_0.47         fastmap_1.1.1     withr_3.0.1      
[29] stringr_1.5.1     generics_0.1.3    fs_1.5.2          vctrs_0.6.1      
[33] sass_0.4.9        grid_4.1.0        rprojroot_2.0.4   tidyselect_1.2.0 
[37] glue_1.6.2        R6_2.5.1          fansi_1.0.4       rmarkdown_2.28   
[41] farver_2.1.1      magrittr_2.0.3    splines_4.1.0     scales_1.3.0     
[45] promises_1.2.0.1  htmltools_0.5.8.1 colorspace_2.1-0  httpuv_1.6.9     
[49] labeling_0.4.3    utf8_1.2.3        stringi_1.7.12    munsell_0.5.1    
[53] cachem_1.0.7