dynverse / dynmethods
Showing 4 of 12 files from the diff.

@@ -25,7 +25,7 @@
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ti_angle <- function(
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    dimred = "pca"
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) {
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  create_ti_method_container(container_id = "dynverse/ti_angle:v0.9.9.01")(
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  create_ti_method_container(container_id = "dynverse/ti_angle:v0.9.9.02")(
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    dimred = dimred
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  )
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}

@@ -19,7 +19,7 @@
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#' 
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#' @param distance_method A character string indicating which
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#' correlationcoefficient (or covariance) is to be computed. One of "pearson",
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#' "kendall", or "spearman". Domain: {spearman, pearson, kendall}. Default:
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#' "kendall", or "spearman". Domain: {spearman, pearson, cosine}. Default:
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#' spearman. Format: character.
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#' @param ndim The number of dimensions in the new space. Domain: U(2, 20).
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#' Default: 3. Format: integer.
@@ -36,8 +36,6 @@
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#' @param smoother `principal_curve` parameter; choice of smoother. Domain:
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#' {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format:
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#' character.
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#' @param sparse Whether or not to use sparse MDS dimensionality reduction, for
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#' datasets with large amounts of cells. Default: TRUE. Format: logical.
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#' 
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#' @keywords method
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#' 
@@ -51,8 +49,7 @@
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    thresh = 0.001,
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    maxit = 10L,
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    stretch = 0,
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    smoother = "smooth_spline",
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    sparse = TRUE
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    smoother = "smooth_spline"
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) {
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  create_ti_method_container(container_id = "dynverse/ti_scorpius:v1.0.0.01")(
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    distance_method = distance_method,
@@ -61,8 +58,7 @@
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    thresh = thresh,
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    maxit = maxit,
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    stretch = stretch,
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    smoother = smoother,
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    sparse = sparse
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    smoother = smoother
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  )
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}
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@@ -18,7 +18,8 @@
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#' trajectories. Nature Methods 14, 979–982.
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#' 
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#' @param reduction_method A character string specifying the algorithm to use for
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#' dimensionality reduction. Domain: {ICA}. Default: ICA. Format: character.
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#' dimensionality reduction. Domain: {DDRTree}. Default: DDRTree. Format:
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#' character.
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#' @param max_components The dimensionality of the reduced space. Domain: U(2,
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#' 20). Default: 2. Format: integer.
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#' @param norm_method Determines how to transform expression values prior to
@@ -40,14 +41,14 @@
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#' \code{\link[dynwrap:infer_trajectories]{infer_trajectory}}
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#' @export
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ti_monocle_ddrtree <- function(
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    reduction_method = "ICA",
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    reduction_method = "DDRTree",
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    max_components = 2L,
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    norm_method = "log",
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    auto_param_selection = TRUE,
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    filter_features = TRUE,
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    filter_features_mean_expression = 0.1
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) {
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  create_ti_method_container(container_id = "dynverse/ti_monocle_ddrtree:v0.9.9.01")(
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  create_ti_method_container(container_id = "dynverse/ti_monocle_ddrtree:v0.9.9.02")(
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    reduction_method = reduction_method,
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    max_components = max_components,
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    norm_method = norm_method,

@@ -17,6 +17,7 @@
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#' N., Purdom, E., Dudoit, S., 2018. Slingshot: cell lineage and pseudotime
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#' inference for single-cell transcriptomics. BMC Genomics 19.
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#' 
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#' @param cluster_method . Domain: {pam, clara}. Default: pam. Format: character.
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#' @param ndim The number of dimensions in the new space. Domain: U(2, 100).
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#' Default: 20. Format: integer.
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#' @param shrink Logical or numeric between 0 and 1, determines whether and how
@@ -58,6 +59,7 @@
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#' \code{\link[dynwrap:infer_trajectories]{infer_trajectory}}
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#' @export
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ti_slingshot <- function(
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    cluster_method = "pam",
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    ndim = 20L,
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    shrink = 1L,
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    reweight = TRUE,
@@ -68,7 +70,8 @@
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    smoother = "smooth.spline",
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    shrink.method = "cosine"
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) {
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  create_ti_method_container(container_id = "dynverse/ti_slingshot:v1.0.2")(
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  create_ti_method_container(container_id = "dynverse/ti_slingshot:v1.0.3")(
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    cluster_method = cluster_method,
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    ndim = ndim,
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    shrink = shrink,
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    reweight = reweight,
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