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Merged
rcorces merged 6 commits into from
Oct 10, 2022
Merged

Dev trajectory #1673

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cfc6127
allow saving of trajectory DF
rcorces Oct 10, 2022
b8c79e1
typo
rcorces Oct 10, 2022
957d670
update param def
rcorces Oct 10, 2022
c8b9071
update warning message for clarity
rcorces Oct 10, 2022
c0544b7
update output message
rcorces Oct 10, 2022
c29cf9d
bugfix
rcorces Oct 10, 2022
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15 changes: 15 additions & 0 deletions R/Trajectory.R
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,8 @@
#' @param useAll A boolean describing whether to use cells outside of trajectory groups for post-fitting procedure.
#' @param dof The number of degrees of freedom to be used in the spline fit. See `stats::smooth.spline()` for more information.
#' @param spar The sparsity to be used in the spline fit. See `stats::smooth.spline()` for more information.
#' @param saveDF A full or relative path to use for creating a `.RDS` R object file containing a DataFrame with additional information about the trajectory.
#' This includes the distance of each cell to the splines of the trajectory and the corresponding indicies returned by `nabor::knn`.
#' @param force A boolean value indicating whether to force the trajactory indicated by `name` to be overwritten if it already exists in the given `ArchRProject`.
#' @param seed A number to be used as the seed for random number generation for trajectory creation.
#' @param logFile The path to a file to be used for logging ArchR output.
Expand All @@ -48,6 +50,7 @@ addTrajectory <- function(
useAll = FALSE,
dof = 250,
spar = 1,
saveDF = NULL,
force = FALSE,
seed = 1,
logFile = createLogFile("addTrajectory")
Expand All @@ -64,6 +67,7 @@ addTrajectory <- function(
.validInput(input = useAll, name = "useAll", valid = c("boolean"))
.validInput(input = dof, name = "dof", valid = c("integer"))
.validInput(input = spar, name = "spar", valid = c("numeric"))
.validInput(input = saveDF, name = "saveDF", valid = c("character", "null"))
.validInput(input = force, name = "force", valid = c("boolean"))
.validInput(input = seed, name = "seed", valid = c("integer"))
.validInput(input = logFile, name = "logFile", valid = c("character"))
Expand Down Expand Up @@ -246,6 +250,17 @@ addTrajectory <- function(
force = force
)

if(!is.null(saveDF)){
tryCatch(
expr = {
.logMessage(paste0("Writing trajectory data frame object to ",saveDF), logFile = logFile, verbose = TRUE)
saveRDS(object = dfTrajectory3, file = saveDF)
},
error = function(e){
.logMessage("Warning! Unable to write to file designated by saveDF. Skipping trajectory DataFrame output.", logFile = logFile, verbose = TRUE)
}
)
}
.endLogging(logFile = logFile)

ArchRProj
Expand Down