Merge pull request #43 from hancockinformatics/devel

Merge Devel 0.99.805

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ABCindex
 Title: A Shiny app to calculate ABCI for checkerboard assays
-Version: 0.99.802
+Version: 0.99.805
 Authors@R:
   person(given = "Travis",
          family = "Blimkie",

NEWS.md

@@ -1,3 +1,11 @@
+# ABCindex v0.99.805
+
+## Changes
+
+* Edited screenshot images in help pages
+* Concentrations now show in proper numeric order, when replicates don't share all concentrations
+
+
 # ABCindex v0.99.802
 
 ## Changes

R/2_upload.R

@@ -683,20 +683,16 @@ plate_reader_single <- function(file, sheet, ext) {
       ) %>%
       mutate(rows = x[3, 1], cols = x[1, 3], .before = 1)
 
-    levels_rows <- sort(unique(as.numeric(df4$rows_conc)))
-    levels_cols <- sort(unique(as.numeric(df4$cols_conc)))
-
     df4 %>%
-      mutate(
-        well = wells,
-        rows_conc = factor(rows_conc, levels = levels_rows),
-        cols_conc = factor(cols_conc, levels = levels_cols),
-        bio = as.numeric(bio)
-      ) %>%
+      mutate(well = wells, bio = as.numeric(bio)) %>%
       select(well, starts_with("cols"), starts_with("rows"), bio)
   }) %>%
     purrr::set_names(~paste0(sheet, "_p", seq(length(.x)))) %>%
-    bind_rows(.id = "replicate")
+    bind_rows(.id = "replicate") %>%
+    mutate(
+      cols_conc = forcats::fct_inseq(cols_conc),
+      rows_conc = forcats::fct_inseq(rows_conc)
+    )
 
   return(d5)
 }

R/3_results.R

@@ -2006,10 +2006,12 @@ writer_xlsx <- function(x, filename) {
     df_clean <- df %>%
       select(cols_conc, rows_conc, abci_avg) %>%
       distinct(cols_conc, rows_conc, .keep_all = TRUE) %>%
-      tidyr::pivot_wider(
-        names_from = "cols_conc",
-        values_from = "abci_avg"
+      mutate(
+        cols_conc = as.numeric(as.character(cols_conc)),
+        rows_conc = as.numeric(as.character(rows_conc))
       ) %>%
+      arrange(cols_conc, rows_conc) %>%
+      tidyr::pivot_wider(names_from = "cols_conc", values_from = "abci_avg") %>%
       tibble::column_to_rownames("rows_conc")
 
     addWorksheet(wb, nm)