manuscript_subsampling
Jenna Hershberger
2021-02-12
Last updated: 2021-04-30
Checks: 7 0
Knit directory: CassavaNIRS/
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Introduction
Prior to this script, run server_subsampling_generalized.R and server_subsample_plsr.R. Then convert the output Rds to a df.
library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──✓ ggplot2 3.3.3 ✓ purrr 0.3.4
✓ tibble 3.1.1 ✓ dplyr 1.0.5
✓ tidyr 1.1.2 ✓ stringr 1.4.0
✓ readr 1.4.0 ✓ forcats 0.5.0── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()library(ggpubr)
library(magrittr)
Attaching package: 'magrittr'The following object is masked from 'package:purrr':
set_namesThe following object is masked from 'package:tidyr':
extractiwanthue <- c("#c84d4c","#c77c3f","#d19f32","#647e3a","#61b858","#4db5a4",
"#6585cc","#975fc7","#c575a1","#cf4391")
namekey <- read.csv("data/TrialNameKey.csv") %>%
rename(Trial = Abbreviated.Trial.Name) subsamp_input <- read.csv("output/subsampling_prediction_results_2021.csv") %>%
full_join(namekey) %>%
mutate(`Subsample type` = case_when(
str_detect(studyName, "19.") ~ "Homogenized sample",
!str_detect(studyName, "19.") & str_detect(studyName, "UYT") ~ "Homogenized sample",
!str_detect(studyName, "19.") & !str_detect(studyName, "UYT") ~ "Roots"),
num_samp_fct = as.factor(number_samples)) Joining, by = "studyName"subsamp_input %>%
group_by(studyName) %>%
summarize(max(number_samples))# A tibble: 10 x 2
studyName `max(number_samples)`
<fct> <int>
1 17.CASS.PYT.49.setA.IB 6
2 17.GS.C3.PYT.80.IB 6
3 18.CASS.PYT.52.IB 6
4 18.GS.C2.setA.UYT.36.IB 2
5 18.GS.C2.setB.UYT.36.IB 2
6 19.CASS.PYT.52.IK 6
7 19.CMSSurveyVarieties.AYT.33.IB 6
8 19.GS.C2.UYT.36.setA.IB 10
9 19.GS.C2.UYT.36.setB.IB 10
10 19.GS.C4B.PYT.500.IK 6subsample.df <- subsamp_input %>%
filter(`Subsample type` == "Homogenized sample") %>%
drop_na() %>%
mutate(num_samp_fct = fct_reorder(num_samp_fct, number_samples))
subsample_plot <- subsample.df %>%
ggplot(aes(x = num_samp_fct, y = R2p, fill = Trial)) +
geom_boxplot() + facet_grid(cols = vars(Trial)) + theme_bw() +
scale_fill_manual(values = iwanthue[c(4:10)], name = "Trial") +
coord_cartesian(ylim = c(0, 1)) +
labs(fill = "Trial", x = "Number of samples", y = expression("R"["p"]^2)) +
theme(legend.position = "none")
subsample_plot
| Version | Author | Date |
|---|---|---|
| 88fee14 | Jenna Hershberger | 2021-04-30 |
root_plot <- subsamp_input %>%
filter(`Subsample type` == "Roots") %>%
drop_na() %>%
mutate(num_samp_fct = fct_reorder(num_samp_fct, number_samples)) %>%
ggplot(aes(x = num_samp_fct, y = R2p, fill = Trial)) +
geom_boxplot() + facet_grid(cols = vars(Trial)) + theme_bw() +
scale_fill_manual(values = iwanthue[c(1:3)], name = "Trial") +
coord_cartesian(ylim = c(0, 1)) +
labs(fill = "Trial", x = "Number of roots", y = expression("R"["p"]^2))+
theme(legend.position = "none")
root_plot
| Version | Author | Date |
|---|---|---|
| 88fee14 | Jenna Hershberger | 2021-04-30 |
split.fig <- ggarrange(root_plot, subsample_plot,
labels = c("A", "B"),
nrow = 2,
widths = c(0.6, 1))
split.fig
| Version | Author | Date |
|---|---|---|
| 88fee14 | Jenna Hershberger | 2021-04-30 |
ggsave(plot = split.fig, filename = "output/Figure5_Subsamples.png",
units = "in", height = 9, width = 12)
sessionInfo()R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin18.2.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.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] magrittr_2.0.1 ggpubr_0.4.0 forcats_0.5.0 stringr_1.4.0
[5] dplyr_1.0.5 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[9] tibble_3.1.1 ggplot2_3.3.3 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 jsonlite_1.7.2 carData_3.0-4 modelr_0.1.8
[5] assertthat_0.2.1 cellranger_1.1.0 yaml_2.2.1 pillar_1.6.0
[9] backports_1.2.1 glue_1.4.2 digest_0.6.27 promises_1.1.1
[13] ggsignif_0.6.0 rvest_0.3.6 colorspace_2.0-0 cowplot_1.1.1
[17] htmltools_0.5.1 httpuv_1.5.5 pkgconfig_2.0.3 broom_0.7.3
[21] haven_2.3.1 scales_1.1.1 whisker_0.4 openxlsx_4.2.3
[25] later_1.1.0.1 rio_0.5.16 git2r_0.28.0 generics_0.1.0
[29] farver_2.1.0 car_3.0-10 ellipsis_0.3.1 withr_2.4.2
[33] cli_2.4.0 crayon_1.4.1 readxl_1.3.1 evaluate_0.14
[37] fs_1.5.0 fansi_0.4.2 rstatix_0.6.0 xml2_1.3.2
[41] foreign_0.8-72 tools_3.5.2 data.table_1.13.6 hms_1.0.0
[45] lifecycle_1.0.0 munsell_0.5.0 reprex_0.3.0 zip_2.1.1
[49] compiler_3.5.2 rlang_0.4.10 grid_3.5.2 rstudioapi_0.13
[53] labeling_0.4.2 rmarkdown_2.6 gtable_0.3.0 abind_1.4-5
[57] DBI_1.1.1 curl_4.3 R6_2.5.0 lubridate_1.7.9.2
[61] knitr_1.29 utf8_1.2.1 rprojroot_2.0.2 stringi_1.5.3
[65] Rcpp_1.0.6 vctrs_0.3.7 dbplyr_2.0.0 tidyselect_1.1.0
[69] xfun_0.20