Interactive app for SM and ST coordinate alignment

Shiny app allowing for manual alignment of SM pixel coordinates to the same coordinate system of the provided ST data.

Usage

AlignSpatialOmics(
  sm.data,
  st.data,
  msi.pixel.multiplier = 20,
  image.res = "lowres",
  continous_cols = NULL,
  catagorical_cols = NULL,
  fov = "fov",
  image.slice = "slice1",
  shiny.host = "0.0.0.0",
  shiny.port = 4698,
  verbose = FALSE
)

Arguments

sm.data

SpaMTP Seurat Object containing SM data

st.data

SpaMTP Seurat Object containing ST data

msi.pixel.multiplier

Numeric value defining a scale.factor to multiple each SM pixel coordinates by (default = 20).

image.res

Character string of the corresponding ST image scale factor to use (default = "lowres").

continous_cols

Vector of colours to use for plotting continuous data. If NULL, the colour map "Reds" will be used (default = NULL).

catagorical_cols

Vector of colours to use for plotting categorical data (default = NULL).

fov

Character string matching the name of the SM FOV to use for plotting (default = "fov").

image.slice

Character string matching the ST image slice name to use for plotting (default = "slice1").

shiny.host

Character string of the shiny host network interface that the Shiny application will listen on when run (default = "0.0.0.0").

shiny.port

Numeric 4 digit number defining the port that the Shiny application will listen to when run (default = 4698).

verbose

Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = FALSE).

Value

A SpaMTP Seurat Object containing SM data with transformed coordinated to match the aligned ST data

Examples

utils::str(formals(AlignSpatialOmics))
#> Dotted pair list of 11
#>  $ sm.data             : symbol 
#>  $ st.data             : symbol 
#>  $ msi.pixel.multiplier: num 20
#>  $ image.res           : chr "lowres"
#>  $ continous_cols      : NULL
#>  $ catagorical_cols    : NULL
#>  $ fov                 : chr "fov"
#>  $ image.slice         : chr "slice1"
#>  $ shiny.host          : chr "0.0.0.0"
#>  $ shiny.port          : num 4698
#>  $ verbose             : logi FALSE
# SM_Transformed <- AlignSpatialOmics(SM.data, ST.data)