From 6032c6baba1231304ca1460feb1812bf4f2826e0 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Tue, 7 Feb 2017 18:23:46 -0500
Subject: [PATCH] BUG: Remove duplicate control rows

---
 analysis-only_overlap.R | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/analysis-only_overlap.R b/analysis-only_overlap.R
index fafebac..47ff2f2 100644
--- a/analysis-only_overlap.R
+++ b/analysis-only_overlap.R
@@ -1,5 +1,6 @@
 suppressPackageStartupMessages({
     library(tidyverse)
+    library(magrittr)
     library(readxl)
     library(stringr)
     library(methods) # For Rscript per http://stackoverflow.com/a/41797025
@@ -27,26 +28,21 @@ wells_control_plate504 <- tibble::tribble(
         well = c("C03", "C22", "D12", "D13", "E05", "E20", "F11",
                  "F14", "G07", "G18", "H09", "H16", "I09", "I16",
                  "J07", "J18", "K11", "K14", "L05", "L20", "M12",
-                 "M13", "N03", "N22")))
+                 "M13", "N03", "N22"))) %>%
+    rename(symbol_504 = symbol) %>% # Prepare for join.
+    mutate(plate = 504) %>%
+    arrange(well)
 ## FIXME: Need to confirm what type of control Thread is.
 wells_layout <-
     read_excel(files_plate, sheet = 3) %>%
     setNames(tolower(names(.))) %>%
     select(plate, well, `symbol(s)`, `fbgn(s)`, amplicon) %>%
     rename(symbol = `symbol(s)`,
-           fbgn = `fbgn(s)`)
-
-wells_control_comparison <- merge(
-    wells_layout %>% filter(well %in% wells_control_plate504$well,
-                            plate %in% c(501:504, 507)) %>%
-    select(-fbgn, -amplicon) %>% spread(plate, symbol),
-    wells_control_plate504  %>% rename(`504_new` = symbol)) %>%
-    .[, order(colnames(.))] %>% select(well, everything())
-write_csv(wells_control_comparison, "plate504-different-controls.csv")
-
+           fbgn = `fbgn(s)`) %>% arrange(plate, well)
 wells_layout %<>%
-    bind_rows(mutate(wells_control_plate504, plate = 504)) %>%
-    arrange(plate, well) %>%
+    left_join(wells_control_plate504) %>%
+    mutate(symbol = ifelse(is.na(symbol_504), symbol, symbol_504)) %>%
+    select(-symbol_504) %>%
     mutate(control = ifelse(
                symbol %in% c("CAL1", "FACT", "Rho1"), ## Rho1 gives binucleates
                "positive", NA)) %>%