Nothing
R/methods.R
In nanny: High-Level Data Analysis and Manipulation in 'tidyverse' Style
Defines functions
.cluster_elements
#' Get clusters of elements (e.g., elements or features)
#'
#' \lifecycle{maturing}
#'
#' @description cluster_elements() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and identify clusters in the data.
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name cluster_elements
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#' @param .feature The name of the feature column (normally features)
#' @param .value The name of the column including the numerical value the clustering is based on (normally feature value)
#'
#' @param method A character string. The cluster algorithm to use, ay the moment k-means is the only algorithm included.
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#' @param action A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
#' @param ... Further parameters passed to the function kmeans
#'
#' @details identifies clusters in the data, normally of elements.
#' This function returns a tibble with additional columns for the cluster annotation.
#' At the moment only k-means clustering is supported, the plan is to introduce more clustering methods.
#'
#' @return A tbl object with additional columns with cluster labels
#'
#' @examples
#'
#'
#' cluster_elements(mtcars_tidy, car_model, feature, value, method="kmeans", centers = 2)
#'
#' @docType methods
#' @rdname cluster_elements-methods
#' @export
#'
setGeneric("cluster_elements", function(.data,
.element,
.feature,
.value,
method,
of_elements = TRUE,
transform = NULL,
action = "add",
...)
standardGeneric("cluster_elements"))
# Set internal
.cluster_elements = function(.data,
.element,
.feature,
.value,
method ,
of_elements = TRUE,
transform = NULL,
action = "add",
...)
{
# Comply with CRAN NOTES
. = NULL
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
# # Check if data rectangular
# ifelse_pipe(
# (.) %>% check_if_data_rectangular(!!.element,!!.feature,!!.value, type = "soft"),
# ~ .x %>% eliminate_sparse_features(!!.feature)
# ) %>%
if (method == "kmeans") {
if (action == "add"){
.data %>%
dplyr::left_join(
(.) %>%
get_clusters_kmeans_bulk(
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
of_elements = of_elements,
transform = transform,
...
),
by = quo_names(.element)
)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(
.data %>%
get_clusters_kmeans_bulk(
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
of_elements = of_elements,
transform = transform,
...
),
by = quo_names(.element)
)
}
else if (action == "only")
get_clusters_kmeans_bulk(
.data,
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
of_elements = of_elements,
transform = transform,
...
)
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
# else if (method == "SNN") {
# if (action == "add"){
#
# .data %>%
# dplyr::left_join(
# (.) %>%
# get_clusters_SNN_bulk(
# .value = !!.value,
# .element = !!.element,
# .feature = !!.feature,
# of_elements = of_elements,
# transform = transform,
# ...
# )
# )
#
# }
# else if (action == "get"){
#
# .data %>%
#
# # Selecting the right columns
# select(
# !!.element,
# get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
# ) %>%
# distinct() %>%
#
# dplyr::left_join(
# .data %>%
# get_clusters_SNN_bulk(
# .value = !!.value,
# .element = !!.element,
# .feature = !!.feature,
# of_elements = of_elements,
# transform = transform,
# ...
# )
# )
#
# }
#
# else if (action == "only")
# get_clusters_SNN_bulk(
# .data,
# .value = !!.value,
# .element = !!.element,
# .feature = !!.feature,
# of_elements = of_elements,
# transform = transform,
# ...
# )
# else
# stop(
# "nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
# )
# }
else
stop("nanny says: the only supported methods are \"kmeans\" ")
}
#' cluster_elements
#' @docType methods
#' @rdname cluster_elements-methods
#' @return A tbl object with additional columns with cluster labels
#'
setMethod("cluster_elements", "spec_tbl_df", .cluster_elements)
#' cluster_elements
#' @docType methods
#' @rdname cluster_elements-methods
#' @return A tbl object with additional columns with cluster labels
#'
setMethod("cluster_elements", "tbl_df", .cluster_elements)
#' Dimension reduction of the feature value data
#'
#' \lifecycle{maturing}
#'
#' @description reduce_dimensions() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and calculates the reduced dimensional space of the feature value. The functions available are PCA, MDS (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), tSNE (Laurens van der Maaten, 2009)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name reduce_dimensions
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#' @param .feature The name of the feature column (normally features)
#' @param .value The name of the column including the numerical value the clustering is based on (normally feature value)
#'
#' @param method A character string. The dimension reduction algorithm to use (PCA, MDS, tSNE).
#' @param top An integer. How many top genes to select for dimensionality reduction
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param .dims A list of integer vectors corresponding to principal components of interest (e.g., list(1:2, 3:4, 5:6))
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#' @param scale A boolean for method="PCA", this will be passed to the `prcomp` function. It is not included in the ... argument because although the default for `prcomp` if FALSE, it is advisable to set it as TRUE.
#' @param action A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
#' @param ... Further parameters passed to the function prcomp if you choose method="PCA" or Rtsne if you choose method="tSNE"
#'
#' @details This function reduces the dimensions of the feature values.
#' It can use multi-dimensional scaling (MDS) of principal component analysis (PCA).
#'
#' @return A tbl object with additional columns for the reduced dimensions
#'
#'
#' @examples
#'
#'
#' reduce_dimensions(mtcars_tidy, car_model, feature, value, method="PCA")
#'
#' reduce_dimensions(mtcars_tidy, car_model, feature, value, method="MDS")
#'
#' reduce_dimensions(mtcars_tidy, car_model, feature, value, method="tSNE")
#'
#'
#'
#' @docType methods
#' @rdname reduce_dimensions-methods
#' @export
#'
#'
setGeneric("reduce_dimensions", function(.data,
.element,
.feature,
.value,
method,
.dims = 2,
top = Inf,
of_elements = TRUE,
transform = NULL,
scale = TRUE,
action = "add",
...)
standardGeneric("reduce_dimensions"))
# Set internal
.reduce_dimensions = function(.data,
.element,
.feature,
.value,
method,
.dims = 2,
top = Inf,
of_elements = TRUE,
transform = NULL,
scale = TRUE,
action = "add",
...)
{
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
if (method == "MDS") {
.data_processed =
.data %>%
get_reduced_dimensions_MDS_bulk(
.value = !!.value,
.dims = .dims,
.element = !!.element,
.feature = !!.feature,
top = top,
of_elements = of_elements,
transform = transform,
...
)
if (action == "add"){
.data %>% dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
else if (method == "PCA") {
.data_processed =
.data %>%
get_reduced_dimensions_PCA_bulk(
.value = !!.value,
.dims = .dims,
.element = !!.element,
.feature = !!.feature,
top = top,
of_elements = of_elements,
transform = transform,
scale = scale,
...
)
if (action == "add"){
.data %>%
dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
else if (method == "tSNE") {
.data_processed =
.data %>%
get_reduced_dimensions_TSNE_bulk(
.value = !!.value,
.dims = .dims,
.element = !!.element,
.feature = !!.feature,
top = top,
of_elements = of_elements,
transform = transform,
...
)
if (action == "add"){
.data %>%
dplyr::left_join(.data_processed, by = quo_names(.element) ) %>%
reattach_internals(.data_processed)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(.data_processed, by = quo_names(.element) ) %>%
reattach_internals(.data_processed)
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
else
stop("nanny says: method must be either \"MDS\" or \"PCA\"")
}
#' reduce_dimensions
#' @docType methods
#' @rdname reduce_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions
setMethod("reduce_dimensions", "spec_tbl_df", .reduce_dimensions)
#' reduce_dimensions
#' @docType methods
#' @rdname reduce_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions
setMethod("reduce_dimensions", "tbl_df", .reduce_dimensions)
#' Rotate two dimensions (e.g., principal components) of an arbitrary angle
#'
#' \lifecycle{maturing}
#'
#' @description rotate_dimensions() takes as imput a `tbl` formatted as | <DIMENSION 1> | <DIMENSION 2> | <...> | and calculates the rotated dimensional space of the feature value.
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name rotate_dimensions
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#'
#' @param dimension_1_column A character string. The column of the dimension 1
#' @param dimension_2_column A character string. The column of the dimension 2
#' @param rotation_degrees A real number between 0 and 360
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param dimension_1_column_rotated A character string. The column of the rotated dimension 1 (optional)
#' @param dimension_2_column_rotated A character string. The column of the rotated dimension 2 (optional)
#' @param action A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
#'
#' @details This function to rotate two dimensions such as the reduced dimensions.
#'
#' @return A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.
#'
#'
#' @examples
#'
#' mtcars_tidy_MDS = reduce_dimensions(mtcars_tidy, car_model, feature, value, method="MDS")
#'
#' rotate_dimensions(mtcars_tidy_MDS, `Dim1`, `Dim2`, .element = car_model, rotation_degrees = 45)
#'
#'
#' @docType methods
#' @rdname rotate_dimensions-methods
#' @export
#'
setGeneric("rotate_dimensions", function(.data,
dimension_1_column,
dimension_2_column,
rotation_degrees,
.element,
of_elements = TRUE,
dimension_1_column_rotated = NULL,
dimension_2_column_rotated = NULL,
action = "add")
standardGeneric("rotate_dimensions"))
# Set internal
.rotate_dimensions = function(.data,
dimension_1_column,
dimension_2_column,
rotation_degrees,
.element,
of_elements = TRUE,
dimension_1_column_rotated = NULL,
dimension_2_column_rotated = NULL,
action = "add")
{
# Get column names
.element = enquo(.element)
# Parse other colnames
dimension_1_column = enquo(dimension_1_column)
dimension_2_column = enquo(dimension_2_column)
dimension_1_column_rotated = enquo(dimension_1_column_rotated)
dimension_2_column_rotated = enquo(dimension_2_column_rotated)
# Set default col names for rotated dimensions if not set
if (quo_is_null(dimension_1_column_rotated))
dimension_1_column_rotated = as.symbol(sprintf(
"%s rotated %s",
quo_names(dimension_1_column),
rotation_degrees
))
if (quo_is_null(dimension_2_column_rotated))
dimension_2_column_rotated = as.symbol(sprintf(
"%s rotated %s",
quo_names(dimension_2_column),
rotation_degrees
))
.data_processed =
get_rotated_dimensions(
.data,
dimension_1_column = !!dimension_1_column,
dimension_2_column = !!dimension_2_column,
rotation_degrees = rotation_degrees,
.element = !!.element,
of_elements = of_elements,
dimension_1_column_rotated = !!dimension_1_column_rotated,
dimension_2_column_rotated = !!dimension_2_column_rotated
)
if (action == "add"){
.data %>%
dplyr::left_join( .data_processed, by = quo_names(.element) )
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_specific_annotation_columns(.data, !!.element)
) %>%
distinct() %>%
dplyr::left_join( .data_processed, by = quo_names(.element) )
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
#' rotate_dimensions
#' @docType methods
#' @rdname rotate_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.
setMethod("rotate_dimensions", "spec_tbl_df", .rotate_dimensions)
#' rotate_dimensions
#' @docType methods
#' @rdname rotate_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.
setMethod("rotate_dimensions", "tbl_df", .rotate_dimensions)
#' Drop redundant elements (e.g., elements) for which feature (e.g., feature/gene) aboundances are correlated
#'
#' \lifecycle{maturing}
#'
#' @description remove_redundancy() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | for correlation method, and returns a `tbl` with dropped elements (e.g., elements). The backend function used is widyr::pairwise_cor (David Robinson, 2020)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name remove_redundancy
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#' @param .feature The name of the feature column (normally features)
#' @param .value The name of the column including the numerical value the clustering is based on (normally feature value)
#'
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#' @param correlation_threshold A real number between 0 and 1. For correlation based calculation.
#' @param top An integer. How many top genes to select for correlation based method
#'
#'
#' @details This function removes redundant elements from the original data set (e.g., elements or features). For example, if we want to define cell-type specific signatures with low element redundancy. This function returns a tibble with dropped recundant elements (e.g., elements). Two redundancy estimation approaches are supported: (i) removal of highly correlated clusters of elements (keeping a representative) with method="correlation"; (ii) removal of most proximal element pairs in a reduced dimensional space.
#'
#' @return A tbl object with with dropped recundant elements (e.g., elements).
#'
#' @examples
#'
#'
#'
#' remove_redundancy(mtcars_tidy, car_model, feature, value)
#'
#'
#' @docType methods
#' @rdname remove_redundancy-methods
#' @export
#'
#'
setGeneric("remove_redundancy", function(.data,
.element,
.feature,
.value,
of_elements = TRUE,
correlation_threshold = 0.9,
top = Inf,
transform = NULL)
standardGeneric("remove_redundancy"))
# Set internal
.remove_redundancy = function(.data,
.element,
.feature,
.value,
of_elements = TRUE,
correlation_threshold = 0.9,
top = Inf,
transform = NULL)
{
# Make col names
.value = enquo(.value)
.element = enquo(.element)
.feature = enquo(.feature)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
remove_redundancy_elements_through_correlation(
.data,
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
correlation_threshold = correlation_threshold,
top = top,
of_elements = of_elements,
transform = transform
)
}
#' remove_redundancy
#' @docType methods
#' @rdname remove_redundancy-methods
#' @return A tbl object with with dropped recundant elements (e.g., elements).
setMethod("remove_redundancy", "spec_tbl_df", .remove_redundancy)
#' remove_redundancy
#' @docType methods
#' @rdname remove_redundancy-methods
#' @return A tbl object with with dropped recundant elements (e.g., elements).
setMethod("remove_redundancy", "tbl_df", .remove_redundancy)
#' Extract selected-column-wise information
#'
#' \lifecycle{maturing}
#'
#' @description subset() takes as imput a `tbl` and returns a `tbl` with only selected-column-related columns
#'
#' @importFrom magrittr "%>%"
#'
#' @name subset
#'
#' @param .data A `tbl`
#' @param .column The name of the column of interest
#'
#'
#' @details This functon extracts only selected-column-related information for downstream analysis (e.g., visualisation). It is disruptive in the sense that it cannot be passed anymore to nanny function.
#'
#' @return A `tbl` object
#'
#'
#'
#'
#' @examples
#'
#' subset(mtcars_tidy,car_model)
#'
#'
#' @docType methods
#' @rdname subset-methods
#' @export
#'
#'
setGeneric("subset", function(.data,
.column)
standardGeneric("subset"))
# Set internal
.subset = function(.data,
.column) {
# Make col names
.column = enquo(.column)
# Check if column present
if(quo_names(.column) %in% colnames(.data) %>% all %>% `!`)
stop("nanny says: some of the .column specified do not exist in the input data frame.")
.data %>%
# Selecting the right columns
select( !!.column, get_specific_annotation_columns(.data, !!.column) ) %>%
distinct()
}
#' subset
#' @docType methods
#' @rdname subset-methods
#' @return A `tbl` object
setMethod("subset", "spec_tbl_df", .subset)
#' subset
#' @docType methods
#' @rdname subset-methods
#' @return A `tbl` object
setMethod("subset", "tbl_df", .subset)
#' subset
#' @docType methods
#' @rdname subset-methods
#' @return A `tbl` object
setMethod("subset", "tbl", .subset)
#' Nest according to selected-column-wise information
#'
#' \lifecycle{maturing}
#'
#' @description nest_subset() takes as imput a `tbl` and returns a nested `tbl` according to only selected-column-related columns
#'
#' @importFrom magrittr "%>%"
#' @importFrom tidyr nest
#' @importFrom purrr map
#' @importFrom purrr imap
#' @importFrom rlang set_names
#' @importFrom tidyselect eval_select
#'
#' @name nest_subset
#'
#' @param .data A `tbl`
#' @param ... The name of the columns of interest
#' @param .names_sep Deprecated by tidyr
#'
#'
#' @details This function extracts only selected-column-related information for downstream analysis (e.g., visualisation). It is disruptive in the sense that it cannot be passed anymore to nanny function.
#'
#' @return A `tbl` object
#'
#'
#'
#'
#' @examples
#'
#' nest_subset(mtcars_tidy,data = -car_model)
#'
#'
#' @docType methods
#' @rdname nest_subset-methods
#' @export
#'
#'
setGeneric("nest_subset", function(.data, ..., .names_sep = NULL)
standardGeneric("nest_subset"))
# Set internal
.nest_subset = function(.data, ..., .names_sep = NULL) {
# Make col names - from tidyr
cols = enquos(...)
cols <- map(cols, ~ names(eval_select(.x, .data)))
cols <- map(cols, set_names)
if (!is.null(.names_sep)) cols <- imap(cols, strip_names, .names_sep)
asis <- setdiff(names(.data), unlist(cols))
# Check if column present
if(asis %in% colnames(.data) %>% all %>% `!`)
stop("nanny says: some of the .column specified do not exist in the input data frame.")
# Get my subset columns
asis_subset = asis %>% c(get_specific_annotation_columns(.data, !!as.symbol(asis)))
# Apply nest on those
tidyr::nest(.data, data = -c(asis_subset))
}
#' nest_subset
#' @docType methods
#' @rdname nest_subset-methods
#' @return A `tbl` object
setMethod("nest_subset", "spec_tbl_df", .nest_subset)
#' nest_subset
#' @docType methods
#' @rdname nest_subset-methods
#' @return A `tbl` object
setMethod("nest_subset", "tbl_df", .nest_subset)
#' nest_subset
#' @inheritParams nest_subset
#' @return A `tbl` object
setMethod("nest_subset", "tbl", .nest_subset)
#' Impute feature value if missing from element-feature pairs
#'
#' \lifecycle{maturing}
#'
#' @description impute_missing() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with an edditional adjusted value column. This method uses scaled counts if present.
#'
#' @importFrom rlang enquo
#' @importFrom rlang is_formula
#' @importFrom magrittr "%>%"
#'
#' @name impute_missing
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column
#' @param .feature The name of the feature/gene column
#' @param .value The name of the feature/gene value column
#' @param .formula A formula with no response variable, representing the desired linear model where the first covariate is the factor of interest and the second covariate is the unwanted variation (of the kind ~ factor_of_intrest + batch)
#'
#'
#' @details This function imputes the value of missing element-feature pair using the median of the element group defined by the formula
#'
#' @return A `tbl` non-sparse value
#'
#'
#'
#'
#' @examples
#'
#' impute_missing(mtcars_tidy, car_model, feature, value, ~1)
#'
#' @docType methods
#' @rdname impute_missing-methods
#'
#' @export
#'
#'
setGeneric("impute_missing", function(.data,
.element,
.feature,
.value,
.formula)
standardGeneric("impute_missing"))
# Set internal
.impute_missing = function(.data,
.element,
.feature,
.value,
.formula)
{
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Sanity check formula
formula_error_message = "nanny says: your formula does not look like one. Check it with rlang::is_formula"
if(
tryCatch(!is_formula(.formula), error=function(x) stop(formula_error_message))
) stop(formula_error_message)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
fill_NA_using_formula(
.data,
.formula,
.element = !!.element,
.feature = !!.feature,
.value = !!.value)
}
#' impute_missing
#' @docType methods
#' @rdname impute_missing-methods
#' @return A `tbl` with imputed abundnce
setMethod("impute_missing", "spec_tbl_df", .impute_missing)
#' impute_missing
#' @docType methods
#' @rdname impute_missing-methods
#' @return A `tbl` with imputed abundnce
setMethod("impute_missing", "tbl_df", .impute_missing)
#' Fill feature value if missing from element-feature pairs
#'
#' \lifecycle{maturing}
#'
#' @description fill_missing() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with an edditional adjusted value column. This method uses scaled counts if present.
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name fill_missing
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column
#' @param .feature The name of the feature/gene column
#' @param .value The name of the feature/gene value column
#' @param fill_with A numerical value with which fill the mssing data points
#'
#' @details This function fills the value of missing element-feature pair using the median of the element group defined by the formula
#'
#' @return A `tbl` non-sparse value
#'
#'
#'
#'
#' @examples
#'
#' fill_missing(mtcars_tidy, car_model, feature, value, fill_with = 0)
#'
#'
#' @docType methods
#' @rdname fill_missing-methods
#'
#' @export
#'
#'
setGeneric("fill_missing", function(.data,
.element,
.feature,
.value,
fill_with)
standardGeneric("fill_missing"))
# Set internal
.fill_missing = function(.data,
.element,
.feature,
.value,
fill_with)
{
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Check the value is set
if(length(fill_with)==0) stop("nanny says: the argument fill_with must not be empty.")
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
fill_NA_using_value(
.data,
.element = !!.element,
.feature = !!.feature,
.value = !!.value,
fill_with)
}
#' fill_missing
#' @docType methods
#' @rdname fill_missing-methods
#' @return A `tbl` with filled abundance
setMethod("fill_missing", "spec_tbl_df", .fill_missing)
#' fill_missing
#' @docType methods
#' @rdname fill_missing-methods
#' @return A `tbl` with filled abundance
setMethod("fill_missing", "tbl_df", .fill_missing)
#' Permute columns and nest data for each permutation
#'
#' \lifecycle{maturing}
#'
#' @description permute_nest() takes as input a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with data nested for each permutation. The package used in the backend is gtools (Gregory R. Warnes, Ben Bolker, and Thomas Lumley, 2020)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#' @importFrom gtools permutations
#'
#' @name permute_nest
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .names_from The columns to build the permutations on (e.g., c(col1, col2))
#' @param .values_from The columns to be nested for each permutation (e.g., c(col3, col4, col5))
#'
#' @details ...
#'
#' @return A nested `tbl`
#'
#'
#'
#'
#' @examples
#'
#' permute_nest(mtcars_tidy, car_model, c(feature,value))
#'
#' @docType methods
#' @rdname permute_nest-methods
#'
#' @export
#'
#'
setGeneric("permute_nest", function(.data, .names_from, .values_from)
standardGeneric("permute_nest"))
# Set internal
.permute_nest = function(.data, .names_from, .values_from){
# Comply with CRAN NOTES
. = NULL
run = NULL
# V1 = NULL
# V2 - NULL
# Column names
.names_from = enquo(.names_from)
.values_from = enquo(.values_from)
# Check if multiple column inputted
if(length(quo_names(.names_from))>1)
stop("nanny says: At the moment only one names column can be used to permute")
factor_levels = .data %>% pull(!!.names_from) %>% unique
.data %>%
pull(!!.names_from) %>%
unique() %>%
as.character() %>%
permutations(n = length(.), r = 2, v = .) %>%
as_tibble() %>%
unite("run", c("V1", "V2"), remove = FALSE, sep="___") %>%
gather(which, !!.names_from, -run) %>%
select(-which) %>%
left_join(.data %>% select(!!.names_from, !!.values_from), by = quo_names(.names_from)) %>%
nest(data = -run) %>%
separate(run, sprintf("%s_%s", quo_names(.names_from), 1:2 ), sep="___") %>%
# Introduce levels
mutate_at(vars(1:2),function(x) factor(x, levels = factor_levels))
}
#' permute_nest
#' @docType methods
#' @rdname permute_nest-methods
#' @return A `tbl` with filled abundance
setMethod("permute_nest", "spec_tbl_df", .permute_nest)
#' permute_nest
#' @docType methods
#' @rdname permute_nest-methods
#' @return A `tbl` with filled abundance
setMethod("permute_nest", "tbl_df", .permute_nest)
#' Combine columns and nest data for each permutation
#'
#' \lifecycle{maturing}
#'
#' @description combine_nest() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with data nested for each combination The package used in the backend is gtools (Gregory R. Warnes, Ben Bolker, and Thomas Lumley, 2020)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#' @importFrom gtools combinations
#'
#' @name combine_nest
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .names_from The columns to build the permutations on (e.g., c(col1, col2))
#' @param .values_from The columns to be nested for each permutation (e.g., c(col3, col4, col5))
#'
#' @details ...
#'
#' @return A nested `tbl`
#'
#'
#'
#'
#' @examples
#'
#' combine_nest(mtcars_tidy, car_model, c(feature,value))
#'
#'
#' @docType methods
#' @rdname combine_nest-methods
#'
#' @export
#'
#'
setGeneric("combine_nest", function(.data, .names_from, .values_from)
standardGeneric("combine_nest"))
# Set internal
.combine_nest = function(.data, .names_from, .values_from){
# Comply with CRAN NOTES
. = NULL
run = NULL
# V1 = NULL
# V2 - NULL
# Column names
.names_from = enquo(.names_from)
.values_from = enquo(.values_from)
factor_levels = .data %>% pull(!!.names_from) %>% unique
# Check if multiple column inputted
if(length(quo_names(.names_from))>1)
stop("nanny says: At the moment only one names column can be used to permute")
factor_levels = .data %>% pull(!!.names_from) %>% unique
.data %>%
pull(!!.names_from) %>%
unique() %>%
as.character() %>%
gtools::combinations(n = length(.), r = 2, v = .) %>%
as_tibble() %>%
unite("run", c("V1", "V2"), remove = FALSE, sep="___") %>%
gather(which, !!.names_from, -run) %>%
select(-which) %>%
left_join(.data %>% select(!!.names_from, !!.values_from), by = quo_names(.names_from)) %>%
nest(data = -run) %>%
separate(run, sprintf("%s_%s", quo_names(.names_from), 1:2), sep="___") %>%
# Introduce levels
mutate_at(vars(1:2),function(x) factor(x, levels = factor_levels))
}
#' combine_nest
#' @docType methods
#' @rdname combine_nest-methods
#' @return A `tbl` with filled abundance
setMethod("combine_nest", "spec_tbl_df", .combine_nest)
#' combine_nest
#' @docType methods
#' @rdname combine_nest-methods
#' @return A `tbl` with filled abundance
setMethod("combine_nest", "tbl_df", .combine_nest)
#' Keep top variable features across elements
#'
#' \lifecycle{maturing}
#'
#' @description keep_variable() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with the filtered most variable features. The formula used is from limma::plotMDS (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name keep_variable
#'
#' @param .data A `tbl`
#' @param .element A character name of the element column
#' @param .feature A character name of the transcript/gene column
#' @param .value A character name of the read count column
#' @param top An integer. How many top genes to select
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#'
#' @details ...
#'
#' @return A `tbl` with filtered features
#'
#'
#'
#'
#' @examples
#'
#' keep_variable(mtcars_tidy, car_model, feature, value, top=10)
#'
#'
#' @docType methods
#' @rdname keep_variable-methods
#'
#' @export
#'
#'
setGeneric("keep_variable", function(.data,
.element,
.feature,
.value,
top = Inf,
transform = NULL)
standardGeneric("keep_variable"))
# Set internal
.keep_variable = function(.data,
.element,
.feature,
.value,
top = Inf,
transform = NULL) {
# Comply with CRAN NOTES
. = NULL
value = NULL
variable = NULL
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Check that column names do not have the reserved pattern "___"
if(.data %>% colnames %>% grep("___", .) %>% length %>% `>` (0))
stop("nanny says: your column names cannot include the pattern \"___\" that is reserved for internal manipulation")
# Manage Inf
top = min(top, .data %>% select(!!.feature) %>% distinct %>% nrow)
x =
.data %>%
select(!!.element, !!.feature, !!.value) %>%
distinct %>%
# Check if tranfrom is needed
ifelse_pipe(
is_function(transform),
~ .x %>%
mutate(!!.value := !!.value %>% transform()) %>%
# Check is log introduced -Inf
ifelse_pipe(pull(.,!!.value) %>% min %>% equals(-Inf),
~ stop(
"nanny says: you applied a transformation that introduced negative infinite .value, was it log? If so please use log1p."
))
) %>%
pivot_wider(names_from = !!.element, values_from = !!.value, names_sep = "___") %>%
as_matrix(rownames = !!.feature)
s <- rowMeans((x - rowMeans(x)) ^ 2)
o <- order(s, decreasing = TRUE)
x <- x[o[1L:top], , drop = FALSE]
.data %>% inner_join(
rownames(x) %>% as_tibble() %>% separate(col = value, into = quo_names(.feature), sep = "___")
)
}
#' keep_variable
#' @docType methods
#' @rdname keep_variable-methods
#' @return A `tbl` with filled abundance
setMethod("keep_variable", "spec_tbl_df", .keep_variable)
#' keep_variable
#' @docType methods
#' @rdname keep_variable-methods
#' @return A `tbl` with filled abundance
setMethod("keep_variable", "tbl_df", .keep_variable)
#' Keep rows corresponding of a lower triangular matrix built from two columns
#'
#' \lifecycle{maturing}
#'
#' @description lower_triangular() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a filtered `tbl`
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name lower_triangular
#'
#' @param .data A `tbl`
#' @param .col1 A column name
#' @param .col2 A column name
#' @param .value A column names of the value column
#'
#' @details ...
#'
#' @return A `tbl` with filtered rows
#'
#'
#'
#'
#' @examples
#'
#' library(dplyr)
#' library(purrr)
#' library(tidyr)
#'
#' mtcars_tidy_permuted =
#' mtcars_tidy %>%
#' filter(feature == "mpg") %>%
#' head(5) %>%
#' permute_nest(car_model, c(feature,value))
#'
#' mtcars_tidy_permuted %>%
#' # Summarise mpg
#' mutate(data = map(data, ~ .x %>% summarise(mean(value)))) %>%
#' unnest(data) %>%
#'
#' # Lower triangular
#' lower_triangular(car_model_1, car_model_2, `mean(value)`)
#'
#' @docType methods
#' @rdname lower_triangular-methods
#'
#' @export
#'
#'
setGeneric("lower_triangular", function(.data, .col1, .col2, .value)
standardGeneric("lower_triangular"))
# Set internal
.lower_triangular = function(.data, .col1, .col2, .value){
# Comply with CRAN NOTES
. = NULL
# Column names
.col1 = enquo(.col1)
.col2 = enquo(.col2)
.value = enquo(.value)
#levs = .data %>% pull(!!.col1) %>% levels
.data %>%
# Check if duplicated elements
error_if_duplicated_genes(!!.col1,!!.col2,!!.value) %>%
select(!!.col1, !!.col2, !!.value) %>%
spread(!!.col2 , !!.value) %>%
as_matrix(rownames = quo_names(.col1)) %>%
# Drop upper triangular
{ ma = (.); ma[lower.tri(ma)] <- NA; ma} %>%
as_tibble(rownames = quo_names(.col1)) %>%
gather(!!.col2, !!.value, -!!.col1) %>%
mutate(
# !!.col1 := factor(!!.col1, levels = levs),
# !!.col2 := factor(!!.col2, levels = levs),
!!.col1 := factor(!!.col1),
!!.col2 := factor(!!.col2),
) %>%
drop_na %>%
# Reattach col1 col2 wise annotation
left_join(.data %>% select(-!!.value) %>% subset(c(!!.col1, !!.col2)), by=c(quo_name(.col1), quo_name(.col2)))
}
#' lower_triangular
#' @docType methods
#' @rdname lower_triangular-methods
#' @return A `tbl` with filled abundance
setMethod("lower_triangular", "spec_tbl_df", .lower_triangular)
#' lower_triangular
#' @docType methods
#' @rdname lower_triangular-methods
#' @return A `tbl` with filled abundance
setMethod("lower_triangular", "tbl_df", .lower_triangular)
#' Get matrix from tibble
#'
#' @import dplyr
#' @import tidyr
#' @importFrom magrittr set_rownames
#' @importFrom rlang quo_is_null
#' @importFrom rlang quo_is_symbolic
#' @importFrom purrr when
#'
#'
#' @param .data A tibble
#' @param rownames A character string of the rownames
#' @param do_check A boolean
#' @param sep_rownames A character with which multiple columns are united if rownames is a column array (e.g., rownames = c(col1, col2))
#'
#' @return A matrix
#'
#' @examples
#'
#' library(dplyr)
#' library(tidyr)
#' select(mtcars_tidy, car_model, feature, value) %>%
#' spread(feature, value) %>%
#' as_matrix(rownames = car_model)
#'
#' @docType methods
#' @rdname as_matrix-methods
#'
#' @export
setGeneric("as_matrix", function(.data,
rownames = NULL,
do_check = TRUE,
sep_rownames = "___")
standardGeneric("as_matrix"))
# Set internal
.as_matrix = function(.data,
rownames = NULL,
do_check = TRUE,
sep_rownames = "___") {
# Comply with CRAN NOTES
variable = NULL
rownames = enquo(rownames)
.data %>%
# Through warning if data frame is not numerical beside the rownames column (if present)
ifelse_pipe(
do_check &&
.data %>%
# If rownames defined eliminate it from the data frame
ifelse_pipe(!quo_is_null(rownames), ~ .x %>% select(-!!rownames), ~ .x) %>%
dplyr::summarise_all(class) %>%
tidyr::gather(variable, class) %>%
pull(class) %>%
unique() %>%
`%in%`(c("numeric", "integer")) %>% `!`() %>% any(),
~ {
warning("nanny says: there are NON-numerical columns, the matrix will NOT be numerical")
.x
}
) %>%
# If rownames multiple enquo (e.g., c(col1, col2)) merge them
when(!quo_is_null(rownames) ~ (.) %>% unite(col = "rn", !!rownames, sep = sep_rownames), ~ (.)) %>%
as.data.frame() %>%
# Deal with rownames column if present
ifelse_pipe(
!quo_is_null(rownames),
~ .x %>%
set_rownames(.x %>% pull(rn)) %>%
select(-rn)
) %>%
# Convert to matrix
as.matrix()
}
#' as_matrix
#' @docType methods
#' @rdname as_matrix-methods
#' @return A `tbl` with filled abundance
setMethod("as_matrix", "spec_tbl_df", .as_matrix)
#' as_matrix
#' @docType methods
#' @rdname as_matrix-methods
#' @return A `tbl` with filled abundance
setMethod("as_matrix", "tbl_df", .as_matrix)
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Defines functions .cluster_elements
#' Get clusters of elements (e.g., elements or features)
#'
#' \lifecycle{maturing}
#'
#' @description cluster_elements() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and identify clusters in the data.
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name cluster_elements
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#' @param .feature The name of the feature column (normally features)
#' @param .value The name of the column including the numerical value the clustering is based on (normally feature value)
#'
#' @param method A character string. The cluster algorithm to use, ay the moment k-means is the only algorithm included.
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#' @param action A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
#' @param ... Further parameters passed to the function kmeans
#'
#' @details identifies clusters in the data, normally of elements.
#' This function returns a tibble with additional columns for the cluster annotation.
#' At the moment only k-means clustering is supported, the plan is to introduce more clustering methods.
#'
#' @return A tbl object with additional columns with cluster labels
#'
#' @examples
#'
#'
#' cluster_elements(mtcars_tidy, car_model, feature, value, method="kmeans", centers = 2)
#'
#' @docType methods
#' @rdname cluster_elements-methods
#' @export
#'
setGeneric("cluster_elements", function(.data,
.element,
.feature,
.value,
method,
of_elements = TRUE,
transform = NULL,
action = "add",
...)
standardGeneric("cluster_elements"))
# Set internal
.cluster_elements = function(.data,
.element,
.feature,
.value,
method ,
of_elements = TRUE,
transform = NULL,
action = "add",
...)
{
# Comply with CRAN NOTES
. = NULL
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
# # Check if data rectangular
# ifelse_pipe(
# (.) %>% check_if_data_rectangular(!!.element,!!.feature,!!.value, type = "soft"),
# ~ .x %>% eliminate_sparse_features(!!.feature)
# ) %>%
if (method == "kmeans") {
if (action == "add"){
.data %>%
dplyr::left_join(
(.) %>%
get_clusters_kmeans_bulk(
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
of_elements = of_elements,
transform = transform,
...
),
by = quo_names(.element)
)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(
.data %>%
get_clusters_kmeans_bulk(
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
of_elements = of_elements,
transform = transform,
...
),
by = quo_names(.element)
)
}
else if (action == "only")
get_clusters_kmeans_bulk(
.data,
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
of_elements = of_elements,
transform = transform,
...
)
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
# else if (method == "SNN") {
# if (action == "add"){
#
# .data %>%
# dplyr::left_join(
# (.) %>%
# get_clusters_SNN_bulk(
# .value = !!.value,
# .element = !!.element,
# .feature = !!.feature,
# of_elements = of_elements,
# transform = transform,
# ...
# )
# )
#
# }
# else if (action == "get"){
#
# .data %>%
#
# # Selecting the right columns
# select(
# !!.element,
# get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
# ) %>%
# distinct() %>%
#
# dplyr::left_join(
# .data %>%
# get_clusters_SNN_bulk(
# .value = !!.value,
# .element = !!.element,
# .feature = !!.feature,
# of_elements = of_elements,
# transform = transform,
# ...
# )
# )
#
# }
#
# else if (action == "only")
# get_clusters_SNN_bulk(
# .data,
# .value = !!.value,
# .element = !!.element,
# .feature = !!.feature,
# of_elements = of_elements,
# transform = transform,
# ...
# )
# else
# stop(
# "nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
# )
# }
else
stop("nanny says: the only supported methods are \"kmeans\" ")
}
#' cluster_elements
#' @docType methods
#' @rdname cluster_elements-methods
#' @return A tbl object with additional columns with cluster labels
#'
setMethod("cluster_elements", "spec_tbl_df", .cluster_elements)
#' cluster_elements
#' @docType methods
#' @rdname cluster_elements-methods
#' @return A tbl object with additional columns with cluster labels
#'
setMethod("cluster_elements", "tbl_df", .cluster_elements)
#' Dimension reduction of the feature value data
#'
#' \lifecycle{maturing}
#'
#' @description reduce_dimensions() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and calculates the reduced dimensional space of the feature value. The functions available are PCA, MDS (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), tSNE (Laurens van der Maaten, 2009)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name reduce_dimensions
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#' @param .feature The name of the feature column (normally features)
#' @param .value The name of the column including the numerical value the clustering is based on (normally feature value)
#'
#' @param method A character string. The dimension reduction algorithm to use (PCA, MDS, tSNE).
#' @param top An integer. How many top genes to select for dimensionality reduction
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param .dims A list of integer vectors corresponding to principal components of interest (e.g., list(1:2, 3:4, 5:6))
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#' @param scale A boolean for method="PCA", this will be passed to the `prcomp` function. It is not included in the ... argument because although the default for `prcomp` if FALSE, it is advisable to set it as TRUE.
#' @param action A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
#' @param ... Further parameters passed to the function prcomp if you choose method="PCA" or Rtsne if you choose method="tSNE"
#'
#' @details This function reduces the dimensions of the feature values.
#' It can use multi-dimensional scaling (MDS) of principal component analysis (PCA).
#'
#' @return A tbl object with additional columns for the reduced dimensions
#'
#'
#' @examples
#'
#'
#' reduce_dimensions(mtcars_tidy, car_model, feature, value, method="PCA")
#'
#' reduce_dimensions(mtcars_tidy, car_model, feature, value, method="MDS")
#'
#' reduce_dimensions(mtcars_tidy, car_model, feature, value, method="tSNE")
#'
#'
#'
#' @docType methods
#' @rdname reduce_dimensions-methods
#' @export
#'
#'
setGeneric("reduce_dimensions", function(.data,
.element,
.feature,
.value,
method,
.dims = 2,
top = Inf,
of_elements = TRUE,
transform = NULL,
scale = TRUE,
action = "add",
...)
standardGeneric("reduce_dimensions"))
# Set internal
.reduce_dimensions = function(.data,
.element,
.feature,
.value,
method,
.dims = 2,
top = Inf,
of_elements = TRUE,
transform = NULL,
scale = TRUE,
action = "add",
...)
{
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
if (method == "MDS") {
.data_processed =
.data %>%
get_reduced_dimensions_MDS_bulk(
.value = !!.value,
.dims = .dims,
.element = !!.element,
.feature = !!.feature,
top = top,
of_elements = of_elements,
transform = transform,
...
)
if (action == "add"){
.data %>% dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
else if (method == "PCA") {
.data_processed =
.data %>%
get_reduced_dimensions_PCA_bulk(
.value = !!.value,
.dims = .dims,
.element = !!.element,
.feature = !!.feature,
top = top,
of_elements = of_elements,
transform = transform,
scale = scale,
...
)
if (action == "add"){
.data %>%
dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(.data_processed, by = quo_names(.element)) %>%
reattach_internals(.data_processed)
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
else if (method == "tSNE") {
.data_processed =
.data %>%
get_reduced_dimensions_TSNE_bulk(
.value = !!.value,
.dims = .dims,
.element = !!.element,
.feature = !!.feature,
top = top,
of_elements = of_elements,
transform = transform,
...
)
if (action == "add"){
.data %>%
dplyr::left_join(.data_processed, by = quo_names(.element) ) %>%
reattach_internals(.data_processed)
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_x_y_annotation_columns(.data, !!.element,!!.feature, !!.value)$horizontal_cols
) %>%
distinct() %>%
dplyr::left_join(.data_processed, by = quo_names(.element) ) %>%
reattach_internals(.data_processed)
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
else
stop("nanny says: method must be either \"MDS\" or \"PCA\"")
}
#' reduce_dimensions
#' @docType methods
#' @rdname reduce_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions
setMethod("reduce_dimensions", "spec_tbl_df", .reduce_dimensions)
#' reduce_dimensions
#' @docType methods
#' @rdname reduce_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions
setMethod("reduce_dimensions", "tbl_df", .reduce_dimensions)
#' Rotate two dimensions (e.g., principal components) of an arbitrary angle
#'
#' \lifecycle{maturing}
#'
#' @description rotate_dimensions() takes as imput a `tbl` formatted as | <DIMENSION 1> | <DIMENSION 2> | <...> | and calculates the rotated dimensional space of the feature value.
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name rotate_dimensions
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#'
#' @param dimension_1_column A character string. The column of the dimension 1
#' @param dimension_2_column A character string. The column of the dimension 2
#' @param rotation_degrees A real number between 0 and 360
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param dimension_1_column_rotated A character string. The column of the rotated dimension 1 (optional)
#' @param dimension_2_column_rotated A character string. The column of the rotated dimension 2 (optional)
#' @param action A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
#'
#' @details This function to rotate two dimensions such as the reduced dimensions.
#'
#' @return A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.
#'
#'
#' @examples
#'
#' mtcars_tidy_MDS = reduce_dimensions(mtcars_tidy, car_model, feature, value, method="MDS")
#'
#' rotate_dimensions(mtcars_tidy_MDS, `Dim1`, `Dim2`, .element = car_model, rotation_degrees = 45)
#'
#'
#' @docType methods
#' @rdname rotate_dimensions-methods
#' @export
#'
setGeneric("rotate_dimensions", function(.data,
dimension_1_column,
dimension_2_column,
rotation_degrees,
.element,
of_elements = TRUE,
dimension_1_column_rotated = NULL,
dimension_2_column_rotated = NULL,
action = "add")
standardGeneric("rotate_dimensions"))
# Set internal
.rotate_dimensions = function(.data,
dimension_1_column,
dimension_2_column,
rotation_degrees,
.element,
of_elements = TRUE,
dimension_1_column_rotated = NULL,
dimension_2_column_rotated = NULL,
action = "add")
{
# Get column names
.element = enquo(.element)
# Parse other colnames
dimension_1_column = enquo(dimension_1_column)
dimension_2_column = enquo(dimension_2_column)
dimension_1_column_rotated = enquo(dimension_1_column_rotated)
dimension_2_column_rotated = enquo(dimension_2_column_rotated)
# Set default col names for rotated dimensions if not set
if (quo_is_null(dimension_1_column_rotated))
dimension_1_column_rotated = as.symbol(sprintf(
"%s rotated %s",
quo_names(dimension_1_column),
rotation_degrees
))
if (quo_is_null(dimension_2_column_rotated))
dimension_2_column_rotated = as.symbol(sprintf(
"%s rotated %s",
quo_names(dimension_2_column),
rotation_degrees
))
.data_processed =
get_rotated_dimensions(
.data,
dimension_1_column = !!dimension_1_column,
dimension_2_column = !!dimension_2_column,
rotation_degrees = rotation_degrees,
.element = !!.element,
of_elements = of_elements,
dimension_1_column_rotated = !!dimension_1_column_rotated,
dimension_2_column_rotated = !!dimension_2_column_rotated
)
if (action == "add"){
.data %>%
dplyr::left_join( .data_processed, by = quo_names(.element) )
}
else if (action == "get"){
.data %>%
# Selecting the right columns
select(
!!.element,
get_specific_annotation_columns(.data, !!.element)
) %>%
distinct() %>%
dplyr::left_join( .data_processed, by = quo_names(.element) )
}
else if (action == "only") .data_processed
else
stop(
"nanny says: action must be either \"add\" for adding this information to your data frame or \"get\" to just get the information"
)
}
#' rotate_dimensions
#' @docType methods
#' @rdname rotate_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.
setMethod("rotate_dimensions", "spec_tbl_df", .rotate_dimensions)
#' rotate_dimensions
#' @docType methods
#' @rdname rotate_dimensions-methods
#' @return A tbl object with additional columns for the reduced dimensions. additional columns for the rotated dimensions. The rotated dimensions will be added to the original data set as `<NAME OF DIMENSION> rotated <ANGLE>` by default, or as specified in the input arguments.
setMethod("rotate_dimensions", "tbl_df", .rotate_dimensions)
#' Drop redundant elements (e.g., elements) for which feature (e.g., feature/gene) aboundances are correlated
#'
#' \lifecycle{maturing}
#'
#' @description remove_redundancy() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | for correlation method, and returns a `tbl` with dropped elements (e.g., elements). The backend function used is widyr::pairwise_cor (David Robinson, 2020)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name remove_redundancy
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column (normally elements).
#' @param .feature The name of the feature column (normally features)
#' @param .value The name of the column including the numerical value the clustering is based on (normally feature value)
#'
#' @param of_elements A boolean. In case the input is a nanny object, it indicates Whether the element column will be element or feature column
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#' @param correlation_threshold A real number between 0 and 1. For correlation based calculation.
#' @param top An integer. How many top genes to select for correlation based method
#'
#'
#' @details This function removes redundant elements from the original data set (e.g., elements or features). For example, if we want to define cell-type specific signatures with low element redundancy. This function returns a tibble with dropped recundant elements (e.g., elements). Two redundancy estimation approaches are supported: (i) removal of highly correlated clusters of elements (keeping a representative) with method="correlation"; (ii) removal of most proximal element pairs in a reduced dimensional space.
#'
#' @return A tbl object with with dropped recundant elements (e.g., elements).
#'
#' @examples
#'
#'
#'
#' remove_redundancy(mtcars_tidy, car_model, feature, value)
#'
#'
#' @docType methods
#' @rdname remove_redundancy-methods
#' @export
#'
#'
setGeneric("remove_redundancy", function(.data,
.element,
.feature,
.value,
of_elements = TRUE,
correlation_threshold = 0.9,
top = Inf,
transform = NULL)
standardGeneric("remove_redundancy"))
# Set internal
.remove_redundancy = function(.data,
.element,
.feature,
.value,
of_elements = TRUE,
correlation_threshold = 0.9,
top = Inf,
transform = NULL)
{
# Make col names
.value = enquo(.value)
.element = enquo(.element)
.feature = enquo(.feature)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
remove_redundancy_elements_through_correlation(
.data,
.value = !!.value,
.element = !!.element,
.feature = !!.feature,
correlation_threshold = correlation_threshold,
top = top,
of_elements = of_elements,
transform = transform
)
}
#' remove_redundancy
#' @docType methods
#' @rdname remove_redundancy-methods
#' @return A tbl object with with dropped recundant elements (e.g., elements).
setMethod("remove_redundancy", "spec_tbl_df", .remove_redundancy)
#' remove_redundancy
#' @docType methods
#' @rdname remove_redundancy-methods
#' @return A tbl object with with dropped recundant elements (e.g., elements).
setMethod("remove_redundancy", "tbl_df", .remove_redundancy)
#' Extract selected-column-wise information
#'
#' \lifecycle{maturing}
#'
#' @description subset() takes as imput a `tbl` and returns a `tbl` with only selected-column-related columns
#'
#' @importFrom magrittr "%>%"
#'
#' @name subset
#'
#' @param .data A `tbl`
#' @param .column The name of the column of interest
#'
#'
#' @details This functon extracts only selected-column-related information for downstream analysis (e.g., visualisation). It is disruptive in the sense that it cannot be passed anymore to nanny function.
#'
#' @return A `tbl` object
#'
#'
#'
#'
#' @examples
#'
#' subset(mtcars_tidy,car_model)
#'
#'
#' @docType methods
#' @rdname subset-methods
#' @export
#'
#'
setGeneric("subset", function(.data,
.column)
standardGeneric("subset"))
# Set internal
.subset = function(.data,
.column) {
# Make col names
.column = enquo(.column)
# Check if column present
if(quo_names(.column) %in% colnames(.data) %>% all %>% `!`)
stop("nanny says: some of the .column specified do not exist in the input data frame.")
.data %>%
# Selecting the right columns
select( !!.column, get_specific_annotation_columns(.data, !!.column) ) %>%
distinct()
}
#' subset
#' @docType methods
#' @rdname subset-methods
#' @return A `tbl` object
setMethod("subset", "spec_tbl_df", .subset)
#' subset
#' @docType methods
#' @rdname subset-methods
#' @return A `tbl` object
setMethod("subset", "tbl_df", .subset)
#' subset
#' @docType methods
#' @rdname subset-methods
#' @return A `tbl` object
setMethod("subset", "tbl", .subset)
#' Nest according to selected-column-wise information
#'
#' \lifecycle{maturing}
#'
#' @description nest_subset() takes as imput a `tbl` and returns a nested `tbl` according to only selected-column-related columns
#'
#' @importFrom magrittr "%>%"
#' @importFrom tidyr nest
#' @importFrom purrr map
#' @importFrom purrr imap
#' @importFrom rlang set_names
#' @importFrom tidyselect eval_select
#'
#' @name nest_subset
#'
#' @param .data A `tbl`
#' @param ... The name of the columns of interest
#' @param .names_sep Deprecated by tidyr
#'
#'
#' @details This function extracts only selected-column-related information for downstream analysis (e.g., visualisation). It is disruptive in the sense that it cannot be passed anymore to nanny function.
#'
#' @return A `tbl` object
#'
#'
#'
#'
#' @examples
#'
#' nest_subset(mtcars_tidy,data = -car_model)
#'
#'
#' @docType methods
#' @rdname nest_subset-methods
#' @export
#'
#'
setGeneric("nest_subset", function(.data, ..., .names_sep = NULL)
standardGeneric("nest_subset"))
# Set internal
.nest_subset = function(.data, ..., .names_sep = NULL) {
# Make col names - from tidyr
cols = enquos(...)
cols <- map(cols, ~ names(eval_select(.x, .data)))
cols <- map(cols, set_names)
if (!is.null(.names_sep)) cols <- imap(cols, strip_names, .names_sep)
asis <- setdiff(names(.data), unlist(cols))
# Check if column present
if(asis %in% colnames(.data) %>% all %>% `!`)
stop("nanny says: some of the .column specified do not exist in the input data frame.")
# Get my subset columns
asis_subset = asis %>% c(get_specific_annotation_columns(.data, !!as.symbol(asis)))
# Apply nest on those
tidyr::nest(.data, data = -c(asis_subset))
}
#' nest_subset
#' @docType methods
#' @rdname nest_subset-methods
#' @return A `tbl` object
setMethod("nest_subset", "spec_tbl_df", .nest_subset)
#' nest_subset
#' @docType methods
#' @rdname nest_subset-methods
#' @return A `tbl` object
setMethod("nest_subset", "tbl_df", .nest_subset)
#' nest_subset
#' @inheritParams nest_subset
#' @return A `tbl` object
setMethod("nest_subset", "tbl", .nest_subset)
#' Impute feature value if missing from element-feature pairs
#'
#' \lifecycle{maturing}
#'
#' @description impute_missing() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with an edditional adjusted value column. This method uses scaled counts if present.
#'
#' @importFrom rlang enquo
#' @importFrom rlang is_formula
#' @importFrom magrittr "%>%"
#'
#' @name impute_missing
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column
#' @param .feature The name of the feature/gene column
#' @param .value The name of the feature/gene value column
#' @param .formula A formula with no response variable, representing the desired linear model where the first covariate is the factor of interest and the second covariate is the unwanted variation (of the kind ~ factor_of_intrest + batch)
#'
#'
#' @details This function imputes the value of missing element-feature pair using the median of the element group defined by the formula
#'
#' @return A `tbl` non-sparse value
#'
#'
#'
#'
#' @examples
#'
#' impute_missing(mtcars_tidy, car_model, feature, value, ~1)
#'
#' @docType methods
#' @rdname impute_missing-methods
#'
#' @export
#'
#'
setGeneric("impute_missing", function(.data,
.element,
.feature,
.value,
.formula)
standardGeneric("impute_missing"))
# Set internal
.impute_missing = function(.data,
.element,
.feature,
.value,
.formula)
{
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Sanity check formula
formula_error_message = "nanny says: your formula does not look like one. Check it with rlang::is_formula"
if(
tryCatch(!is_formula(.formula), error=function(x) stop(formula_error_message))
) stop(formula_error_message)
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
fill_NA_using_formula(
.data,
.formula,
.element = !!.element,
.feature = !!.feature,
.value = !!.value)
}
#' impute_missing
#' @docType methods
#' @rdname impute_missing-methods
#' @return A `tbl` with imputed abundnce
setMethod("impute_missing", "spec_tbl_df", .impute_missing)
#' impute_missing
#' @docType methods
#' @rdname impute_missing-methods
#' @return A `tbl` with imputed abundnce
setMethod("impute_missing", "tbl_df", .impute_missing)
#' Fill feature value if missing from element-feature pairs
#'
#' \lifecycle{maturing}
#'
#' @description fill_missing() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with an edditional adjusted value column. This method uses scaled counts if present.
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name fill_missing
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .element The name of the element column
#' @param .feature The name of the feature/gene column
#' @param .value The name of the feature/gene value column
#' @param fill_with A numerical value with which fill the mssing data points
#'
#' @details This function fills the value of missing element-feature pair using the median of the element group defined by the formula
#'
#' @return A `tbl` non-sparse value
#'
#'
#'
#'
#' @examples
#'
#' fill_missing(mtcars_tidy, car_model, feature, value, fill_with = 0)
#'
#'
#' @docType methods
#' @rdname fill_missing-methods
#'
#' @export
#'
#'
setGeneric("fill_missing", function(.data,
.element,
.feature,
.value,
fill_with)
standardGeneric("fill_missing"))
# Set internal
.fill_missing = function(.data,
.element,
.feature,
.value,
fill_with)
{
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Check the value is set
if(length(fill_with)==0) stop("nanny says: the argument fill_with must not be empty.")
# Validate data frame
validation(.data, !!.element, !!.feature, !!.value)
fill_NA_using_value(
.data,
.element = !!.element,
.feature = !!.feature,
.value = !!.value,
fill_with)
}
#' fill_missing
#' @docType methods
#' @rdname fill_missing-methods
#' @return A `tbl` with filled abundance
setMethod("fill_missing", "spec_tbl_df", .fill_missing)
#' fill_missing
#' @docType methods
#' @rdname fill_missing-methods
#' @return A `tbl` with filled abundance
setMethod("fill_missing", "tbl_df", .fill_missing)
#' Permute columns and nest data for each permutation
#'
#' \lifecycle{maturing}
#'
#' @description permute_nest() takes as input a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with data nested for each permutation. The package used in the backend is gtools (Gregory R. Warnes, Ben Bolker, and Thomas Lumley, 2020)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#' @importFrom gtools permutations
#'
#' @name permute_nest
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .names_from The columns to build the permutations on (e.g., c(col1, col2))
#' @param .values_from The columns to be nested for each permutation (e.g., c(col3, col4, col5))
#'
#' @details ...
#'
#' @return A nested `tbl`
#'
#'
#'
#'
#' @examples
#'
#' permute_nest(mtcars_tidy, car_model, c(feature,value))
#'
#' @docType methods
#' @rdname permute_nest-methods
#'
#' @export
#'
#'
setGeneric("permute_nest", function(.data, .names_from, .values_from)
standardGeneric("permute_nest"))
# Set internal
.permute_nest = function(.data, .names_from, .values_from){
# Comply with CRAN NOTES
. = NULL
run = NULL
# V1 = NULL
# V2 - NULL
# Column names
.names_from = enquo(.names_from)
.values_from = enquo(.values_from)
# Check if multiple column inputted
if(length(quo_names(.names_from))>1)
stop("nanny says: At the moment only one names column can be used to permute")
factor_levels = .data %>% pull(!!.names_from) %>% unique
.data %>%
pull(!!.names_from) %>%
unique() %>%
as.character() %>%
permutations(n = length(.), r = 2, v = .) %>%
as_tibble() %>%
unite("run", c("V1", "V2"), remove = FALSE, sep="___") %>%
gather(which, !!.names_from, -run) %>%
select(-which) %>%
left_join(.data %>% select(!!.names_from, !!.values_from), by = quo_names(.names_from)) %>%
nest(data = -run) %>%
separate(run, sprintf("%s_%s", quo_names(.names_from), 1:2 ), sep="___") %>%
# Introduce levels
mutate_at(vars(1:2),function(x) factor(x, levels = factor_levels))
}
#' permute_nest
#' @docType methods
#' @rdname permute_nest-methods
#' @return A `tbl` with filled abundance
setMethod("permute_nest", "spec_tbl_df", .permute_nest)
#' permute_nest
#' @docType methods
#' @rdname permute_nest-methods
#' @return A `tbl` with filled abundance
setMethod("permute_nest", "tbl_df", .permute_nest)
#' Combine columns and nest data for each permutation
#'
#' \lifecycle{maturing}
#'
#' @description combine_nest() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with data nested for each combination The package used in the backend is gtools (Gregory R. Warnes, Ben Bolker, and Thomas Lumley, 2020)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#' @importFrom gtools combinations
#'
#' @name combine_nest
#'
#' @param .data A `tbl` formatted as | <element> | <feature> | <value> | <...> |
#' @param .names_from The columns to build the permutations on (e.g., c(col1, col2))
#' @param .values_from The columns to be nested for each permutation (e.g., c(col3, col4, col5))
#'
#' @details ...
#'
#' @return A nested `tbl`
#'
#'
#'
#'
#' @examples
#'
#' combine_nest(mtcars_tidy, car_model, c(feature,value))
#'
#'
#' @docType methods
#' @rdname combine_nest-methods
#'
#' @export
#'
#'
setGeneric("combine_nest", function(.data, .names_from, .values_from)
standardGeneric("combine_nest"))
# Set internal
.combine_nest = function(.data, .names_from, .values_from){
# Comply with CRAN NOTES
. = NULL
run = NULL
# V1 = NULL
# V2 - NULL
# Column names
.names_from = enquo(.names_from)
.values_from = enquo(.values_from)
factor_levels = .data %>% pull(!!.names_from) %>% unique
# Check if multiple column inputted
if(length(quo_names(.names_from))>1)
stop("nanny says: At the moment only one names column can be used to permute")
factor_levels = .data %>% pull(!!.names_from) %>% unique
.data %>%
pull(!!.names_from) %>%
unique() %>%
as.character() %>%
gtools::combinations(n = length(.), r = 2, v = .) %>%
as_tibble() %>%
unite("run", c("V1", "V2"), remove = FALSE, sep="___") %>%
gather(which, !!.names_from, -run) %>%
select(-which) %>%
left_join(.data %>% select(!!.names_from, !!.values_from), by = quo_names(.names_from)) %>%
nest(data = -run) %>%
separate(run, sprintf("%s_%s", quo_names(.names_from), 1:2), sep="___") %>%
# Introduce levels
mutate_at(vars(1:2),function(x) factor(x, levels = factor_levels))
}
#' combine_nest
#' @docType methods
#' @rdname combine_nest-methods
#' @return A `tbl` with filled abundance
setMethod("combine_nest", "spec_tbl_df", .combine_nest)
#' combine_nest
#' @docType methods
#' @rdname combine_nest-methods
#' @return A `tbl` with filled abundance
setMethod("combine_nest", "tbl_df", .combine_nest)
#' Keep top variable features across elements
#'
#' \lifecycle{maturing}
#'
#' @description keep_variable() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a `tbl` with the filtered most variable features. The formula used is from limma::plotMDS (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>)
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name keep_variable
#'
#' @param .data A `tbl`
#' @param .element A character name of the element column
#' @param .feature A character name of the transcript/gene column
#' @param .value A character name of the read count column
#' @param top An integer. How many top genes to select
#' @param transform A function to use to tranforma the data internalli (e.g., log1p)
#'
#' @details ...
#'
#' @return A `tbl` with filtered features
#'
#'
#'
#'
#' @examples
#'
#' keep_variable(mtcars_tidy, car_model, feature, value, top=10)
#'
#'
#' @docType methods
#' @rdname keep_variable-methods
#'
#' @export
#'
#'
setGeneric("keep_variable", function(.data,
.element,
.feature,
.value,
top = Inf,
transform = NULL)
standardGeneric("keep_variable"))
# Set internal
.keep_variable = function(.data,
.element,
.feature,
.value,
top = Inf,
transform = NULL) {
# Comply with CRAN NOTES
. = NULL
value = NULL
variable = NULL
# Get column names
.element = enquo(.element)
.feature = enquo(.feature)
.value = enquo(.value)
# Check that column names do not have the reserved pattern "___"
if(.data %>% colnames %>% grep("___", .) %>% length %>% `>` (0))
stop("nanny says: your column names cannot include the pattern \"___\" that is reserved for internal manipulation")
# Manage Inf
top = min(top, .data %>% select(!!.feature) %>% distinct %>% nrow)
x =
.data %>%
select(!!.element, !!.feature, !!.value) %>%
distinct %>%
# Check if tranfrom is needed
ifelse_pipe(
is_function(transform),
~ .x %>%
mutate(!!.value := !!.value %>% transform()) %>%
# Check is log introduced -Inf
ifelse_pipe(pull(.,!!.value) %>% min %>% equals(-Inf),
~ stop(
"nanny says: you applied a transformation that introduced negative infinite .value, was it log? If so please use log1p."
))
) %>%
pivot_wider(names_from = !!.element, values_from = !!.value, names_sep = "___") %>%
as_matrix(rownames = !!.feature)
s <- rowMeans((x - rowMeans(x)) ^ 2)
o <- order(s, decreasing = TRUE)
x <- x[o[1L:top], , drop = FALSE]
.data %>% inner_join(
rownames(x) %>% as_tibble() %>% separate(col = value, into = quo_names(.feature), sep = "___")
)
}
#' keep_variable
#' @docType methods
#' @rdname keep_variable-methods
#' @return A `tbl` with filled abundance
setMethod("keep_variable", "spec_tbl_df", .keep_variable)
#' keep_variable
#' @docType methods
#' @rdname keep_variable-methods
#' @return A `tbl` with filled abundance
setMethod("keep_variable", "tbl_df", .keep_variable)
#' Keep rows corresponding of a lower triangular matrix built from two columns
#'
#' \lifecycle{maturing}
#'
#' @description lower_triangular() takes as imput a `tbl` formatted as | <element> | <feature> | <value> | <...> | and returns a filtered `tbl`
#'
#' @importFrom rlang enquo
#' @importFrom magrittr "%>%"
#'
#' @name lower_triangular
#'
#' @param .data A `tbl`
#' @param .col1 A column name
#' @param .col2 A column name
#' @param .value A column names of the value column
#'
#' @details ...
#'
#' @return A `tbl` with filtered rows
#'
#'
#'
#'
#' @examples
#'
#' library(dplyr)
#' library(purrr)
#' library(tidyr)
#'
#' mtcars_tidy_permuted =
#' mtcars_tidy %>%
#' filter(feature == "mpg") %>%
#' head(5) %>%
#' permute_nest(car_model, c(feature,value))
#'
#' mtcars_tidy_permuted %>%
#' # Summarise mpg
#' mutate(data = map(data, ~ .x %>% summarise(mean(value)))) %>%
#' unnest(data) %>%
#'
#' # Lower triangular
#' lower_triangular(car_model_1, car_model_2, `mean(value)`)
#'
#' @docType methods
#' @rdname lower_triangular-methods
#'
#' @export
#'
#'
setGeneric("lower_triangular", function(.data, .col1, .col2, .value)
standardGeneric("lower_triangular"))
# Set internal
.lower_triangular = function(.data, .col1, .col2, .value){
# Comply with CRAN NOTES
. = NULL
# Column names
.col1 = enquo(.col1)
.col2 = enquo(.col2)
.value = enquo(.value)
#levs = .data %>% pull(!!.col1) %>% levels
.data %>%
# Check if duplicated elements
error_if_duplicated_genes(!!.col1,!!.col2,!!.value) %>%
select(!!.col1, !!.col2, !!.value) %>%
spread(!!.col2 , !!.value) %>%
as_matrix(rownames = quo_names(.col1)) %>%
# Drop upper triangular
{ ma = (.); ma[lower.tri(ma)] <- NA; ma} %>%
as_tibble(rownames = quo_names(.col1)) %>%
gather(!!.col2, !!.value, -!!.col1) %>%
mutate(
# !!.col1 := factor(!!.col1, levels = levs),
# !!.col2 := factor(!!.col2, levels = levs),
!!.col1 := factor(!!.col1),
!!.col2 := factor(!!.col2),
) %>%
drop_na %>%
# Reattach col1 col2 wise annotation
left_join(.data %>% select(-!!.value) %>% subset(c(!!.col1, !!.col2)), by=c(quo_name(.col1), quo_name(.col2)))
}
#' lower_triangular
#' @docType methods
#' @rdname lower_triangular-methods
#' @return A `tbl` with filled abundance
setMethod("lower_triangular", "spec_tbl_df", .lower_triangular)
#' lower_triangular
#' @docType methods
#' @rdname lower_triangular-methods
#' @return A `tbl` with filled abundance
setMethod("lower_triangular", "tbl_df", .lower_triangular)
#' Get matrix from tibble
#'
#' @import dplyr
#' @import tidyr
#' @importFrom magrittr set_rownames
#' @importFrom rlang quo_is_null
#' @importFrom rlang quo_is_symbolic
#' @importFrom purrr when
#'
#'
#' @param .data A tibble
#' @param rownames A character string of the rownames
#' @param do_check A boolean
#' @param sep_rownames A character with which multiple columns are united if rownames is a column array (e.g., rownames = c(col1, col2))
#'
#' @return A matrix
#'
#' @examples
#'
#' library(dplyr)
#' library(tidyr)
#' select(mtcars_tidy, car_model, feature, value) %>%
#' spread(feature, value) %>%
#' as_matrix(rownames = car_model)
#'
#' @docType methods
#' @rdname as_matrix-methods
#'
#' @export
setGeneric("as_matrix", function(.data,
rownames = NULL,
do_check = TRUE,
sep_rownames = "___")
standardGeneric("as_matrix"))
# Set internal
.as_matrix = function(.data,
rownames = NULL,
do_check = TRUE,
sep_rownames = "___") {
# Comply with CRAN NOTES
variable = NULL
rownames = enquo(rownames)
.data %>%
# Through warning if data frame is not numerical beside the rownames column (if present)
ifelse_pipe(
do_check &&
.data %>%
# If rownames defined eliminate it from the data frame
ifelse_pipe(!quo_is_null(rownames), ~ .x %>% select(-!!rownames), ~ .x) %>%
dplyr::summarise_all(class) %>%
tidyr::gather(variable, class) %>%
pull(class) %>%
unique() %>%
`%in%`(c("numeric", "integer")) %>% `!`() %>% any(),
~ {
warning("nanny says: there are NON-numerical columns, the matrix will NOT be numerical")
.x
}
) %>%
# If rownames multiple enquo (e.g., c(col1, col2)) merge them
when(!quo_is_null(rownames) ~ (.) %>% unite(col = "rn", !!rownames, sep = sep_rownames), ~ (.)) %>%
as.data.frame() %>%
# Deal with rownames column if present
ifelse_pipe(
!quo_is_null(rownames),
~ .x %>%
set_rownames(.x %>% pull(rn)) %>%
select(-rn)
) %>%
# Convert to matrix
as.matrix()
}
#' as_matrix
#' @docType methods
#' @rdname as_matrix-methods
#' @return A `tbl` with filled abundance
setMethod("as_matrix", "spec_tbl_df", .as_matrix)
#' as_matrix
#' @docType methods
#' @rdname as_matrix-methods
#' @return A `tbl` with filled abundance
setMethod("as_matrix", "tbl_df", .as_matrix)
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