Merge pull request #29 from SafetyGraphics/IZ_dev

Iz dev

Author: jwildfire

GetStatistics.R

@@ -1,7 +1,5 @@
 # volcano-plot
 
-Original Developers
+![image](https://user-images.githubusercontent.com/62663896/90043322-efd45b00-dc99-11ea-834c-5633c91ea41d.png)
 
-- Ke Xiao (Boehringer Ingelheim)
-- Hong Wang (Boehringer Ingelheim)
-- Dennis o'Brien (Boehringer Ingelheim)
+Thanks to the team at Boehringer Ingelheim for developing and releasing the initial code for this tool. In particular, thanks to, Hong Wang, Ke Xiao and  Dennis O'Brien.

README.md

@@ -0,0 +1,77 @@
+
+
+```{r}
+
+setwd("~/Desktop/volcano-plot")
+library(scales); library(dplyr); library(tidyr); library(tibble); library(stringr); library(ggplot2); library(cowplot); library(ggpubr)
+select <- dplyr::select; rename <- dplyr::rename; mutate <- dplyr::mutate; 
+summarize <- dplyr::summarize; arrange <- dplyr::arrange; slice <- dplyr::slice; filter <- dplyr::filter; recode<-dplyr::recode
+style <- plotly::style
+```
+
+
+Make test dataset
+```{r}
+# https://github.com/SafetyGraphics/volcano-plot/issues/7
+ae_vars = c("USUBJID", "AESEQ", "AESTDT", "AESTDY", "AEENDT", "AEENDY", "AETERM", "AEDECOD", "AEBODSYS", "AESER", "AEONGO", "AESEV", "AEREL", "AEOUT", "STUDYFL", "TRTEMFL")
+dm_vars = c("SITE", "SITEID", "AGE", "SEX", "RACE", "ARM", "ARMCD", "SBJTSTAT", "RFSTDTC", "RFENDTC", "RFENDY", "SAFFL")
+all_vars = c(ae_vars,dm_vars)
+
+# https://github.com/phuse-org/phuse-scripts/tree/master/data/sdtm/TDF_SDTM_v1.0
+library(haven)
+library(readr)
+adae <- haven::read_xpt("https://github.com/phuse-org/phuse-scripts/raw/master/data/adam/cdisc/adae.xpt") %>% select(USUBJID, TRTEMFL, SAFFL)
+adsl <- haven::read_xpt("https://github.com/phuse-org/phuse-scripts/raw/master/data/adam/cdisc/adsl.xpt")
+ae = read_xpt("data/ae.xpt") %>% select(-STUDYID, -DOMAIN )
+dm = read_xpt("data/dm.xpt")%>% select(-STUDYID, -DOMAIN )
+ds = read_xpt("data/ds.xpt")%>% select(-STUDYID, -DOMAIN ) %>% filter(EPOCH=="TREATMENT" & DSCAT=="DISPOSITION EVENT") %>% select(USUBJID,DSDECOD)
+
+test_data = ae %>% 
+    inner_join(dm,by="USUBJID") %>% 
+    inner_join(adae, by="USUBJID") %>%
+    left_join(ds, by="USUBJID") %>% 
+    rename(AESTDT = AESTDTC, AEENDT = AEENDTC) %>%
+    mutate(AEONGO = ifelse(AEENDT=="","Y","N"),
+           STUDYFL = TRTEMFL, 
+           SITE = SITEID,
+           RFENDTC = as.Date(RFENDTC),
+           AEENDT = as.Date(ifelse(AEENDT=="",NA,AEENDT)),
+           RFENDY = as.Date(RFENDTC) - AEENDT,
+           RFENDY = ifelse(AEENDT<RFENDTC, RFENDY+1, RFENDY),
+           SBJTSTAT = case_when(DSDECOD=="COMPLETED"~"TREATMENT COMPLETED",
+                                !is.na(DSDECOD) & DSDECOD!="COMPLETED"~"DISCONTINUED",
+                                TRUE~"ONGOING"),
+           AEREL = recode(AEREL,"PROBABLE"="Y","REMOTE"="Y","POSSIBLE"="Y","NONE"="N"),
+           AEREL = ifelse(AEREL=="",NA,AEREL))
+
+match_vars = all_vars[which(all_vars %in% colnames(test_data))]
+match_vars
+no_vars = all_vars[which(!all_vars %in% colnames(test_data))]
+no_vars
+
+test_data2 = test_data %>% select(match_vars) %>% group_by_all() %>% slice(1) %>% group_by() %>% as.data.frame() %>%
+    mutate(AESTDT = as.Date(AESTDT), AEENDT = as.Date(AEENDT), RFSTDTC = as.Date(RFSTDTC), RFENDTC = as.Date(RFENDTC))
+write_csv(test_data2, path="data/test_data.csv")
+
+
+```
+
+
+
+Load test data
+```{r}
+
+setwd("~/Desktop/volcano-plot")
+library(scales); library(dplyr); library(tidyr); library(tibble); library(stringr); library(ggplot2); library(cowplot); library(ggpubr)
+select <- dplyr::select; rename <- dplyr::rename; mutate <- dplyr::mutate; 
+summarize <- dplyr::summarize; arrange <- dplyr::arrange; slice <- dplyr::slice; filter <- dplyr::filter; recode<-dplyr::recode
+style <- plotly::style
+```
+
+
+```{r}
+library(data.table)
+
+test_data = fread("data/test_data.csv") %>% as.data.frame() %>%
+    mutate(AESTDT = as.Date(AESTDT), AEENDT = as.Date(AEENDT), RFSTDTC = as.Date(RFSTDTC), RFENDTC = as.Date(RFENDTC))
+```

data/Get Test Data.Rmd

@@ -1,51 +1,53 @@
-################################################################################
-# global.R
-# This R Script declares the required packages for loading the Shiny App, links 
-# other R Scripts with global objects and defines global variables and functions.
-################################################################################
-
-### Declaration of required packages for running the Shiny App smoothly --------
-library(shiny) # version: 1.4.0
-library(shinyjs) # version: 1.1
-library(data.table) # version: 1.12.8
-library(DT) # version: 0.12
-library(ggplot2) # version: 3.2.1
-library(plotly) # version: 4.9.1
-library(scales) # version: 1.1.0
-library(shinycssloaders) # version: 0.3
-library(conflicted) # version: 1.0.4
-library(dplyr) # version: 0.8.3
-library(tidyr) # version: 1.0.2
-library(survival) # version: 3.1-8
-library(survminer) # version: 0.4.6
-library(fmsb) # version: 0.7.0
-
-conflict_prefer("first", "dplyr")
-conflict_prefer("filter", "dplyr")
-# conflict_prefer("layout", "plotly")
-# conflict_prefer("hidden", "shinyjs")
-# conflict_prefer("dataTableOutput", "DT")
-
-
-### Source any R Scripts other than ui.R, server.R and global.R ----------------
-source("volcano_plot.R")
-source("GetStatistics.R")
-
-
-### Definitions of global variables and functions ------------------------------
-# Check that it doesn't match any non-number
-numbers_only <- function(x) !grepl("\\D", x)
-
-fmt_dcimals <- function(decimals = 0) {
-  function(x) format(x, nsmall = decimals, scientific = FALSE)
-}
-
-reverselog_trans <- function(base = exp(1)) {
-  trans <- function(x) -log(x, base)
-  inv <- function(x) base^(-x)
-  trans_new(paste0("reverselog-", format(base)), trans, inv, 
-            log_breaks(base = base), 
-            domain = c(1e-100, Inf))
-}
-
-
+################################################################################
+# global.R
+# This R Script declares the required packages for loading the Shiny App, links 
+# other R Scripts with global objects and defines global variables and functions.
+################################################################################
+
+### Declaration of required packages for running the Shiny App smoothly --------
+library(shiny) # version: 1.4.0
+library(shinyjs) # version: 1.1
+library(data.table) # version: 1.12.8
+library(DT) # version: 0.12
+library(ggplot2) # version: 3.2.1
+library(plotly) # version: 4.9.1
+library(scales) # version: 1.1.0
+library(shinycssloaders) # version: 0.3
+library(conflicted) # version: 1.0.4
+library(dplyr) # version: 0.8.3
+library(tidyr) # version: 1.0.2
+library(survival) # version: 3.1-8
+library(survminer) # version: 0.4.6
+library(fmsb) # version: 0.7.0
+library(shinyWidgets)
+library(cowplot)
+# if function conflicts, default dplyr
+conflict_prefer("first", "dplyr")
+select <- dplyr::select; rename <- dplyr::rename; mutate <- dplyr::mutate; summarize <- dplyr::summarize; arrange <- dplyr::arrange; slice <- dplyr::slice; filter <- dplyr::filter; recode<-dplyr::recode
+style <- plotly::style
+# conflict_prefer("layout", "plotly")
+# conflict_prefer("hidden", "shinyjs")
+# conflict_prefer("dataTableOutput", "DT")
+
+
+### Source any R Scripts other than ui.R, server.R and global.R ----------------
+source("volcano_plot.R")
+source("GetStatistics.R")
+
+
+### Definitions of global variables and functions ------------------------------
+# Check that it doesn't match any non-number
+numbers_only <- function(x) !grepl("\\D", x)
+
+# fmt_dcimals <- function(decimals = 0) {
+#   function(x) format(x, nsmall = decimals, scientific = FALSE)
+# }
+
+reverselog_trans <- function(base = exp(1)) {
+  trans <- function(x) -log(x, base)
+  inv <- function(x) base^(-x)
+  trans_new(paste0("reverselog-", format(base)), trans, inv, 
+            log_breaks(base = base), 
+            domain = c(1e-100, Inf))
+}
+