I've placed testdata.RData and repro.R (the app) on Github
My data wrangling inside the Shiny App execution results in different data (and incorrect) compared to when run outside app. If you execute the app, you will see the following:
If you instead run the code in R, substituting the inputs with the same values like this, you get entirely different results.
testdata %>%
dplyr::filter(trt == trt_list[2]) %>%
dplyr::select(x = log2FoldChange, qx = padj, mylabel) -> x
testdata %>%
dplyr::filter(trt == trt_list[1]) %>%
dplyr::select(y = log2FoldChange, qy = padj, mylabel) -> y
plotdata <- dplyr::left_join(x, y, by = c("mylabel"))
plotdata %>% dplyr::mutate(x = ifelse(is.na(x), 0, x),
y = ifelse(is.na(y), 0, y),
qx = ifelse(is.na(qx), 1, qx),
qy = ifelse(is.na(qy), 1, qy)) %>%
dplyr::mutate(significance = ifelse(plotdata$qx <= .1 & plotdata$qy > .1, "X-Significant",
ifelse(plotdata$qx > .1 & plotdata$qy <= .1, "Y-Significant",
ifelse(plotdata$qx <= .1 & plotdata$qy <= .1, "Both-Significant", "Neither")))) %>%
dplyr::filter(significance != "Neither") -> plotdata
final <- as.data.frame(table(plotdata$significance))
final
Answer is this and is correct:
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shinythemes_1.1.2 DT_0.5 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1 tidyr_0.8.3 tibble_2.1.1
[10] ggplot2_3.1.1 tidyverse_1.2.1 shiny_1.2.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 cellranger_1.1.0 pillar_1.3.1 compiler_3.6.0 later_0.8.0 plyr_1.8.4 tools_3.6.0 digest_0.6.18 lubridate_1.7.4
[10] jsonlite_1.6 nlme_3.1-139 gtable_0.3.0 lattice_0.20-38 pkgconfig_2.0.2 rlang_0.3.1 cli_1.1.0 rstudioapi_0.10 crosstalk_1.0.0
[19] yaml_2.2.0 haven_2.1.0 withr_2.1.2 xml2_1.2.0 httr_1.4.0 htmlwidgets_1.3 hms_0.4.2 generics_0.0.2 grid_3.6.0
[28] tidyselect_0.2.5 glue_1.3.0 R6_2.3.0 readxl_1.3.1 modelr_0.1.4 magrittr_1.5 backports_1.1.4 scales_1.0.0 promises_1.0.1
[37] htmltools_0.3.6 rvest_0.3.3 assertthat_0.2.1 mime_0.6 xtable_1.8-3 colorspace_1.4-1 httpuv_1.4.5.1 stringi_1.2.4 lazyeval_0.2.2
[46] munsell_0.5.0 broom_0.5.2 crayon_1.3.4
...