From caaffbe2de54647ab643b917bb1a36065f4d20c9 Mon Sep 17 00:00:00 2001 From: Travis Blimkie Date: Wed, 3 Apr 2024 12:02:27 -0700 Subject: [PATCH 1/3] Concentrations in cards are now sorted in descending order, as shown in the preview. --- DESCRIPTION | 2 +- R/2_upload.R | 4 ++-- app.R | 6 +++++- 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a118e5e..bd18944 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ABCindex Title: A Shiny app to calculate ABCI for checkerboard assays -Version: 0.99.75 +Version: 0.99.76 Authors@R: person(given = "Travis", family = "Blimkie", diff --git a/R/2_upload.R b/R/2_upload.R index 5c6c7e6..bd37b4d 100644 --- a/R/2_upload.R +++ b/R/2_upload.R @@ -370,13 +370,13 @@ fill_card <- function(expt) { p(strong("Treatment in the columns: "), expt$cols$name), p( tags$b("Detected concentrations: "), - paste(expt$cols$conc, collapse = ", ") + paste(sort(expt$cols$conc, decreasing = TRUE), collapse = ", ") ), hr(), p(strong("Treatment in the rows: "), expt$rows$name), p( strong("Detected concentrations: "), - paste(expt$rows$conc, collapse = ", ") + paste(sort(expt$rows$conc, decreasing = TRUE), collapse = ", ") ), ) } diff --git a/app.R b/app.R index 8e45491..072fca6 100644 --- a/app.R +++ b/app.R @@ -13,7 +13,11 @@ suppressPackageStartupMessages({ app_theme <- bs_theme( version = 5, bootswatch = "cosmo", - base_font = font_collection(font_google("Inter", local = FALSE), "Roboto", "sans-serif"), + base_font = font_collection( + font_google("Inter", local = FALSE), + "Roboto", + "sans-serif" + ), font_scale = 0.9, primary = "#cc002c", secondary = "#373a3c", From fa39f137647ab87a307364bdd0109e197d4d91ae Mon Sep 17 00:00:00 2001 From: Travis Blimkie Date: Wed, 3 Apr 2024 13:37:30 -0700 Subject: [PATCH 2/3] Added check to notify function. --- DESCRIPTION | 2 +- R/2_upload.R | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index bd18944..4a6b6be 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ABCindex Title: A Shiny app to calculate ABCI for checkerboard assays -Version: 0.99.76 +Version: 0.99.77 Authors@R: person(given = "Travis", family = "Blimkie", diff --git a/R/2_upload.R b/R/2_upload.R index bd37b4d..e3a3782 100644 --- a/R/2_upload.R +++ b/R/2_upload.R @@ -413,6 +413,8 @@ make_card <- function(title, height = NULL, class = NULL, content) { #' @return A shiny notification bubble #' notify <- function(id = NULL, list) { + stopifnot(all(c("type", "status", "message", "suggest") %in% names(list))) + showNotification( id = id, type = list$type, From d635a726515b22fc3e55fd613bd9bf70dc1eebdc Mon Sep 17 00:00:00 2001 From: Travis Blimkie Date: Wed, 3 Apr 2024 14:13:46 -0700 Subject: [PATCH 3/3] Added ToC and 'Return to top' links to Help pages. --- DESCRIPTION | 2 +- www/help/help.html | 51 ++++++++++++++++++++++++++++++++++------------ 2 files changed, 39 insertions(+), 14 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4a6b6be..c7ecfa1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ABCindex Title: A Shiny app to calculate ABCI for checkerboard assays -Version: 0.99.77 +Version: 0.99.78 Authors@R: person(given = "Travis", family = "Blimkie", diff --git a/www/help/help.html b/www/help/help.html index cfc0bfa..1df4c7b 100644 --- a/www/help/help.html +++ b/www/help/help.html @@ -3,19 +3,40 @@
-

Help for ABCindex

+

Help for ABCindex

- The first section covers the use of the app. Click - here to jump to the next section, which details - the calculation of the ABCI values. + The first section covers how to use the app, while the second section + details the calculation of ABCI values.

-

How to use ABCindex

+ +

Table of contents

+ + + + +

How to use ABCindex

Interpretation and visualization of checkerboard assays.

-

1. Prepare your data

+

1. Prepare your data

ABCindex takes any form of checkerboard assay data (e.g. crystal violet or TTC) in the same format produced by microplate readers. Data can @@ -46,7 +67,7 @@

1. Prepare your data

Input template -

2. Upload and analyze your data

+

2. Upload and analyze your data

Click "Upload plate data" and select an .xlsx or .ods file formatted as detailed above. An input preview will appear to the right of @@ -75,7 +96,7 @@

2. Upload and analyze your data

tab.

-

3. Create plots from your results

+

3. Create plots from your results

ABCindex lets you visualize two types of information:

  • @@ -123,7 +144,7 @@

    3. Create plots from your results

    be lost, so be sure to save anything you want to keep first!

    -

    Learn more

    +

    Learn more

    @@ -261,6 +282,8 @@

    +

    Return to top

    +
    @@ -272,7 +295,7 @@

    ABCI calculations

    calculates and plots the data.

    -

    Rationale behind ABCindex

    +

    Rationale behind ABCindex

    ABCindex aims to overcome the main challenges presented when evaluating antibiofilm combination therapies and, in more general terms, provide a @@ -325,7 +348,7 @@

    Rationale behind ABCindex

    promising interactions and favourable drug ratios.

    -

    Anti-Biofilm Combination Index

    +

    Anti-Biofilm Combination Index

    The Anti-Biofilm Combination Index (ABCI) is calculated for each specific combination of drug concentrations (i.e., each well on a 96-well plate). @@ -423,7 +446,7 @@

    Anti-Biofilm Combination Index

    -

    Data processing in ABCindex

    +

    Data processing in ABCindex

    Checkerboard data uploaded to ABCindex goes through the following steps:

    @@ -454,7 +477,7 @@

    Data processing in ABCindex

    downloaded in the results spreadsheets.

    -

    Learn more

    +

    Learn more

    @@ -509,5 +532,7 @@

    +

    Return to top

    +