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Commit 9c2154f1 authored by Luke Zappia's avatar Luke Zappia
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Use checkParams and getParams

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R/params.R
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...@@ -127,32 +127,38 @@ splatParams <- function(...) { ...@@ -127,32 +127,38 @@ splatParams <- function(...) {
#' @export #' @export
print.splatParams <- function(x, ...) { print.splatParams <- function(x, ...) {
pp <- list("Global:" = c("(Genes)" = x$nGenes, "(Cells)" = x$nCells, pp <- list("Global:" = c("(Genes)" = "nGenes",
"[Group Cells]" = x$groupCells), "(Cells)" = "nCells",
"Mean:" = c("(Rate)" = x$mean$rate, "(Shape)" = x$mean$shape), "[Group Cells]" = "groupCells"),
"Library size:" = c("(Location)" = x$lib$loc, "Mean:" = c("(Rate)" = "mean.rate",
"(Scale)" = x$lib$scale), "(Shape)" = "mean.shape"),
"Expression outliers:" = c("(Probability)" = x$out$prob, "Library size:" = c("(Location)" = "lib.loc",
"(Lo Probability)" = x$out$loProb, "(Scale)" = "lib.scale"),
"(Location)" = x$out$facLoc, "Exprs outliers:" = c("(Probability)" = "out.prob",
"(Scale)" = x$out$facScale), "(Lo Prob)" = "out.loProb",
"Differential expression:" = c("[Probability]" = x$de$prob, "(Location)" = "out.facLoc",
"[Down Prob]" = x$de$downProb, "(Scale)" = "out.facScale"),
"[Location]" = x$de$facLoc, "Differential exprs:" = c("[Probability]" = "de.prob",
"[Scale]" = x$de$facScale), "[Down Prob]" = "de.downProb",
"BCV:" = c("(Common Disp)" = x$bcv$common, "[Location]" = "de.facLoc",
"(Degrees of Freedom)" = x$bcv$DF), "[Scale]" = "de.facScale"),
"Dropout:" = c("(Present T/F)" = x$dropout$present, "BCV:" = c("(Common Disp)" = "bcv.common",
"(Midpoint)" = x$dropout$mid, "(DoF)" = "bcv.DF"),
"(Shape)" = x$dropout$shape), "Dropout:" = c("(Present T/F)" = "dropout.present",
"Paths:" = c("[From]" = x$path$from, "[Length]" = x$path$length, "(Midpoint)" = "dropout.mid",
"[Skew]" = x$path$skew, "(Shape)" = "dropout.shape"),
"[Non-linear Prob]" = x$path$nonlinearProb, "Paths:" = c("[From]" = "path.from",
"[Sigma Factor]" = x$path$sigmaFac)) "[Length]" = "path.length",
"[Skew]" = "path.skew",
"[Non-linear]" = "path.nonlinearProb",
"[Sigma Factor]" = "path.sigmaFac"))
for (category in names(pp)) { for (category in names(pp)) {
parameters <- getParams(x, pp[[category]])
parameters <- sapply(parameters, paste, collapse = ", ")
names(parameters) <- names(pp[[category]])
cat(category, "\n") cat(category, "\n")
print.default(pp[[category]], print.gap = 2) print(noquote(parameters), print.gap = 2)
cat("\n") cat("\n")
} }
} }
...@@ -205,6 +211,8 @@ setParams <- function(params, ...) { ...@@ -205,6 +211,8 @@ setParams <- function(params, ...) {
} }
} }
checkParams(params)
return(params) return(params)
} }
...@@ -310,13 +318,8 @@ checkParams <- function(params) { ...@@ -310,13 +318,8 @@ checkParams <- function(params) {
for (idx in seq_along(types)) { for (idx in seq_along(types)) {
name <- names(types)[idx] name <- names(types)[idx]
name.split <- strsplit(name, ".", fixed = TRUE)[[1]]
type <- types[idx] type <- types[idx]
if (length(name.split) == 1) { value <- getParams(name)
value <- params[[name]]
} else {
value <- params[[name.split[1]]][[name.split[2]]]
}
# Check vector properties first so we can exclude vectors with an NA # Check vector properties first so we can exclude vectors with an NA
# before the next section # before the next section
...@@ -387,6 +390,8 @@ mergeParams <- function(params1, params2) { ...@@ -387,6 +390,8 @@ mergeParams <- function(params1, params2) {
} }
} }
checkParams()
return(params1) return(params1)
} }
...@@ -405,15 +410,17 @@ defaultParams <- function() { ...@@ -405,15 +410,17 @@ defaultParams <- function() {
params <- splatParams() params <- splatParams()
params <- setParams(params, nGenes = 10000, nCells = 100, params <- setParams(params, nGenes = 10000, nCells = 100,
groupCells = 100, mean.rate = 0.3, mean.shape = 0.4, groupCells = 100, mean.rate = 0.3, mean.shape = 0.4,
lib.loc = 10, lib.scale = 0.5, out.prob = 0.1, lib.loc = 10, lib.scale = 0.5, out.prob = 0.1,
out.loProb = 0.5, out.facLoc = 4, out.facScale = 1, out.loProb = 0.5, out.facLoc = 4, out.facScale = 1,
de.prob = 0.1, de.downProb = 0.5, de.facLoc = 4, de.prob = 0.1, de.downProb = 0.5, de.facLoc = 4,
de.facScale = 1, bcv.common = 0.1, bcv.DF = 25, de.facScale = 1, bcv.common = 0.1, bcv.DF = 25,
dropout.present = TRUE, dropout.mid = 0, dropout.present = TRUE, dropout.mid = 0,
dropout.shape = -1, path.from = 0, dropout.shape = -1, path.from = 0, path.length = 100,
path.length = 100, path.skew = 0.5, path.skew = 0.5, path.nonlinearProb = 0.1,
path.nonlinearProb = 0.1, path.sigmaFac = 0.8) path.sigmaFac = 0.8)
checkParams()
return(params) return(params)
} }
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