get.immap.metadata {celltrackR}

Get Track Metadata from ImmuneMap

Description

Get metadata from tracks obtained from https://immunemap.org and import into celltrackR.

Usage

get.immap.metadata(
  input,
  warn.exclude = TRUE,
  exclude.names = c("points", "cellTypeObject", "date")
)

Arguments

input

a parsed json file obtained with parse.immap.json

warn.exclude

logical: if TRUE (default), warn when key-value pairs in the json (other than those in exclude.names) are being ignored while parsing immunemap json.

exclude.names

if the json contains keys with these names, they are ignored when reading the metadata.

Value

a dataframe with metadata. This function currently only handles metadata with a single value for each track and ignores others (with a warning when warn.exclude=TRUE). column names in the dataframe correspond to the keys in the original json, and values to the values for each track.

Examples

## Read tracks from immunemap online
input <- parse.immap.json( url = "https://api.immunemap.org/video/14/tracks" )
meta.df <- get.immap.metadata( input )

## Repeat but ignore also the 'color' column:
exclude <-  c("points", "cellTypeObject","date", "color")
meta.df <- get.immap.metadata( input, exclude.names = exclude )