custom_shiny: Create Customized spatialHeatmap Shiny Apps

In jianhaizhang/spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Create Customized spatialHeatmap Shiny Apps

Description

This function creates customized spatialHeatmap Shiny Apps with user-provided data, aSVG files, and default parameters by using the spatialHeatmap Shiny App as the template.

Usage

custom_shiny(
  data = NULL,
  db = NULL,
  lis.par = NULL,
  par.tmp = FALSE,
  dld.sgl = NULL,
  dld.mul = NULL,
  dld.vars = NULL,
  data.tmp = TRUE,
  ldg = NULL,
  gallery = NULL,
  about = NULL,
  app.dir = "."
)

Arguments

data	A nested ‘list' of custom data and aSVG files that will be the pre-included examples in the custom App. File paths of each data-aSVG pair should be included in a 'list' that have four slots: 'name', 'display', 'data', and 'svg', e.g. 'lis1 <- list(name=’mus.brain', display='Mouse brain (SHM)', data='./mus_brain.txt', svg='./mus_brain.svg')'. The 'name' will be syntactically valide for R code, while the 'display' will be shown on the user interface, so the latter can include special characters. The 'data' and 'svg' is the file path of numeric data and corresponding aSVG respectively. If multiple aSVGs (e.g. growth stages) correspond to a single numeric data set, the respective paths will be stored in a vector in the 'svg' slot (see example below). After store the data-aSVG pairs in separate 'list's, store these 'list's in another 'list' (nested 'list'), e.g. 'list(lis1, lis2)'. The data and aSVGs in the nested 'list' will be copied to the 'data' folder in the custom App.
db	Paired assay data and aSVGs in a tar file that will be used as a backend database. See write_hdf5.
lis.par	A 'list' of custom parameters of the Shiny App that will be the default when the custom App is launched. See par.tmp. Default is 'NULL' and the default parameters in the spatialHeatmap Shiny App will be inherited.
par.tmp	Logical. If 'TRUE' the default paramters in the spatialHeatmap Shiny App are returned in a 'list', and users can edit these settings then assign the 'list' back to lis.par. Note, only the existing values in the 'list' can be edited and the hierarchy of the 'list' should be preserved. Otherwise, it cannot be recognized by the internal program.
dld.sgl	A 'list' of paired data matrix and single aSVG file, which would be downloadable example dataset on the App for testing. The 'list' consists of paths of the data matrix and aSVG file with name slots of 'data' and 'svg' respectively, e.g. list(data='./data_download.txt', svg='./root_download_shm.svg'). The specified data and aSVG will copied to the 'data' folder in the App.
dld.mul	A ‘list' of paired data matrix and multiple aSVG files, which would be downloadable example dataset on the App for testing. It is the same as 'dld.sgl' except that in the 'svg' slot, multiple aSVG file paths are stored, e.g. 'list(data=’./data_download.txt', svg=c('./root_young_download_shm1.svg', './root_old_download_shm2.svg'))'.
dld.vars	A 'list' of paired data matrix and single aSVG file, which would be downloadable data.tmp dataset on the App for testing. It is the same as 'dld.sgl' except that multiple experimental variables are combined in the data matrix (see package viengettes for details.)
data.tmp	Logical. If 'TRUE' (default), both example data sets in the spatialHeatmap Shiny App and custom data sets in 'data' will be included in the custom App.
ldg, gallery, about	The paths of ".html" files that will be used for the landing, gallery, and about pages in the custom Shiny App respectively. The default is 'NULL', indicating default ".html" files will be used.
app.dir	The directory to create the Shiny App. Default is current work directory ..

Value

If par.tmp==TRUE, the default paramters in spatialHeatmap Shiny App are returned in a 'list'. Otherwise, a customized Shiny App is generated in the path of app.dir.

Author(s)

Jianhai Zhang [e-mail]
Dr. Thomas Girke [e-mail]

References

Jeremy Stephens, Kirill Simonov, Yihui Xie, Zhuoer Dong, Hadley Wickham, Jeffrey Horner, reikoch, Will Beasley, Brendan O'Connor and Gregory R. Warnes (2020). yaml: Methods to Convert R Data to YAML and Back. R package version 2.2.1. https://CRAN.R-project.org/package=yaml
Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2017). shiny: Web Application Framework for R. R package version 1.0.3. https://CRAN.R-project.org/package=shiny

Examples

# The data sets in spatialHeatmap are used for demonstrations.

## Below are demonstrations of simple usage.
# File paths of one data matrix and one aSVG.
data.path1 <- system.file('extdata/shinyApp/data/expr_mouse.txt', package='spatialHeatmap')
svg.path1 <- system.file('extdata/shinyApp/data/mus_musculus.male.svg', 
package='spatialHeatmap')
# Save the file paths in a list with name slots of "name", "display", "data", and "svg".
lis.dat1 <- list(name='Mouse', display='Mouse (SHM)', data=data.path1, svg=svg.path1)
# Create custom Shiny Apps.

if (!dir.exists('~/test_shiny')) dir.create('~/test_shiny')
# Create custom Shiny app by feeding this function these datasets and parameters.
custom_shiny(data=list(lis.dat1), app.dir='~/test_shiny')
# Lauch the app.
shiny::runApp('~/test_shiny/shinyApp') 


## Below are demonstrations of advanced usage. 

# Paths of one data matrix and two aSVGs (two growth stages).
data.path2 <- system.file('extdata/shinyApp/data/random_data_multiple_aSVGs.txt', 
package='spatialHeatmap')
svg.path2.1 <- system.file('extdata/shinyApp/data/arabidopsis.thaliana_organ_shm1.svg', 
package='spatialHeatmap')
svg.path2.2 <- system.file('extdata/shinyApp/data/arabidopsis.thaliana_organ_shm2.svg', 
package='spatialHeatmap')
# Save the file paths in a list with name slots of "name", "display", "data", and "svg".
lis.dat2 <- list(name='growthStage', display='Multiple aSVGs (SHM)',data=data.path2, 
svg=c(svg.path2.1, svg.path2.2))

# Paths of one data matrix with combined variables and one aSVG.
data.path.vars <- system.file('extdata/shinyApp/data/mus_brain_vars_se_shiny.rds', 
package='spatialHeatmap')
svg.path.vars <- system.file('extdata/shinyApp/data/mus_musculus.brain.svg', 
package='spatialHeatmap')
# Save the file paths in a list with name slots of "name", "display", "data", and "svg".
lis.dat.vars <- list(name='multiVariables', display='Multiple variables (SHM)', 
data=data.path.vars, svg=svg.path.vars)

# Paths of one data matrix and one aSVGs for creating downloadable example data sets.
data.path.dld1 <- system.file('extdata/shinyApp/data/expr_mouse.txt', 
package='spatialHeatmap')
svg.path.dld1 <- system.file('extdata/shinyApp/data/mus_musculus.male.svg', 
package='spatialHeatmap')
# Save the file paths in a list with name slots of "name", "display", "data", and "svg".
dld.sgl <- list(data=data.path.dld1, svg=svg.path.dld1)

# For demonstration purpose, the same data and aSVGs are used to make the list for creating 
# downloadable example dataset of two growth stages. 
dld.mul <- list(data=data.path2, svg=c(svg.path2.1, svg.path2.2))

# For demonstration purpose, the same multi-variable data and aSVG are used to create the
# downloadable example multi-variable dataset.
dld.vars <- list(data=data.path.vars, svg=svg.path.vars)

# Retrieve the default parameters in the App template.
lis.par <- custom_shiny(par.tmp=TRUE)
# Change default setting of color scheme in the color key.
lis.par$shm.img['color', ] <- 'yellow,orange,blue'
# The default dataset to show when the app is launched.
lis.par$default.dataset <- 'shoot'

# Store all default data sets in a nested list.
dat.all <- list(lis.dat1, lis.dat2, lis.dat.vars)

# Create custom Shiny Apps.

if (!dir.exists('~/test_shiny')) dir.create('~/test_shiny')
custom_shiny(data=dat.all, lis.par=lis.par, dld.sgl=dld.sgl, dld.mul=dld.mul, dld.vars=dld.vars, 
app.dir='~/test_shiny')
# Lauch the App.
shiny::runApp('~/test_shiny/shinyApp') 


# The customized Shiny App is able to take database backend as well. Examples are 
# demonstrated in the function "write_hdf5".

jianhaizhang/spatialHeatmap documentation built on Nov. 28, 2024, 4:44 p.m.