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https://github.com/Yang-Tang/layoutPlateMod
A shiny module for plotting microplate layout
https://github.com/Yang-Tang/layoutPlateMod
Last synced: 8 days ago
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A shiny module for plotting microplate layout
- Host: GitHub
- URL: https://github.com/Yang-Tang/layoutPlateMod
- Owner: Yang-Tang
- Created: 2016-11-02T10:14:21.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2016-11-02T13:20:44.000Z (about 8 years ago)
- Last Synced: 2024-08-13T07:15:32.715Z (4 months ago)
- Language: R
- Size: 702 KB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- jimsghstars - Yang-Tang/layoutPlateMod - A shiny module for plotting microplate layout (R)
README
# layoutPlateMod
A shiny module for plotting microplate layout
### Introduction
This is a highcharter package based shiny module that can display the layout of a microplate as bubble plot and return infomation of user selected wells.
### Pre-request
This shiny module requires following packages. Please make sure they are installed.
```r
install.package('dplyr')
install.package('tidyr')
install.package('highcharter')
```
### Usage
1. Source the module file
```r
source('layoutPlateMod.R')
```
2. In server function, create a shiny reactive object that contains the microplate layout data to be displayed in dataframe format:
```r
server <- function(input, output) {
# The microplate dataframe should contain at least four columns:
# Well(chr): the well id of microplate (eg, A1, A2, B5, D12)
# Value(num): the value of that well to be displayed as bubble size
# Color_by(chr): the categorical variable that defines the color of bubble
# Label(chr): the label displayed on the bubble
# The dataframe may contain other columns and will be ignored.
microplate <- reactive({
expand.grid(Row = LETTERS[1:8], Col = 1:12, stringsAsFactors = F) %>%
unite(Well, Row, Col, sep = '') %>%
mutate(Value = runif(n()),
Color_by = sample(c('Group A', 'Group B', 'Group C', NA_character_), n(), T),
Label = sample(c(1:5, NA), n(), T)) %>%
sample_frac(0.9) %>%
arrange(Color_by)
})
# other codes
}
```
3. Invoke module in server function and send the microplate data object to the `data` parameter. Set `nrow` and `ncol` to define the type of microplate:
```r
selected <- callModule(loplate, id = 'YOU_MODULE_ID', data = microplate, nrow = 8, ncol = 12)
```
4. Add layout output ui
```r
ui <- fluidPage(
loplateUI('YOU_MODULE_ID')
)
```
5. Run app. Select wells by Click + Dragging or Shift + Click. The module returns a subsetted dataframe according to the selection.
