Commit fc45c368 authored by houyun's avatar houyun
Browse files

clean document

parent ec9c0deb

DESCRIPTION

+0 −1
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@@ -19,7 +19,6 @@ Depends: R (>= 3.5.0) 
Imports: 

    digest,

    dplyr, 

    geomtextpath,

    ggplot2 (>= 3.0.0), 

    glue, 

    grDevices,

NAMESPACE

+0 −46
Original line number Diff line number Diff line 
# Generated by roxygen2: do not edit by hand



S3method("[",marker)

S3method(as_correlate,corr.test)

S3method(as_correlate,data.frame)

S3method(as_correlate,matrix)

S3method(as_correlate,rcorr)

S3method(as_matrix_data,corr.test)

S3method(as_matrix_data,correlate)

S3method(as_matrix_data,data.frame)

S3method(as_matrix_data,default)

S3method(as_matrix_data,grouped_correlate)

S3method(as_matrix_data,matrix)

S3method(as_matrix_data,rcorr)

S3method(as_md_tbl,corr.test)

S3method(as_md_tbl,correlate)

S3method(as_md_tbl,data.frame)

S3method(as_md_tbl,easycorrelation)

S3method(as_md_tbl,grouped_correlate)

S3method(as_md_tbl,grouped_matrix_data)

S3method(as_md_tbl,mantel_tbl)

S3method(as_md_tbl,matrix)

S3method(as_md_tbl,matrix_data)

S3method(as_md_tbl,md_tbl)

S3method(as_md_tbl,pro_tbl)

S3method(as_md_tbl,rcorr)

S3method(c,marker)

S3method(get_order,character)

S3method(get_order,dendrogram)
@@ -44,15 +22,6 @@ S3method(guide_train,guide_child) 
S3method(guide_transform,guide_child)

S3method(length,marker)

S3method(makeContent,markerGrob)

S3method(marker,"magick-image")

S3method(marker,character)

S3method(marker,formula)

S3method(marker,gList)

S3method(marker,ggplot)

S3method(marker,grob)

S3method(marker,list)

S3method(marker,marker)

S3method(marker,raster)

S3method(plot,gggplot)

S3method(print,calc_relimp)

S3method(print,correlate)
@@ -63,26 +32,19 @@ S3method(print,hyplot) 
S3method(print,marker)

S3method(print,matrix_data)

S3method(print,random_forest)

S3method(qcorrplot,cor_md_tbl)

S3method(qcorrplot,data.frame)

S3method(qcorrplot,default)

S3method(qcorrplot,matrix)

S3method(rep_len,marker)

export("%>%")

export("col_names<-")

export("row_names<-")

export(DoughnutGrob)

export(GeomCorr)

export(GeomCurve2)

export(GeomDoughnut)

export(GeomHalfcircle)

export(GeomMark)

export(GeomSquare)

export(Geomshaping)

export(aes)

export(anno_link)

export(as.igraph)

export(as_correlate)

export(as_matrix_data)

export(as_md_tbl)

export(as_tbl_graph)
@@ -95,7 +57,6 @@ export(contain_with) 
export(correlate)

export(dist_func)

export(draw_key_marker)

export(dudi_pca)

export(extract_diag)

export(extract_lower)

export(extract_upper)
@@ -105,11 +66,9 @@ export(filter_func) 
export(gdist)

export(geom_corr)

export(geom_couple)

export(geom_curve2)

export(geom_diag_label)

export(geom_doughnut)

export(geom_ggplot)

export(geom_halfcircle)

export(geom_magic_text)

export(geom_mark)

export(geom_node_doughnut)
@@ -131,13 +90,11 @@ export(make_cluster) 
export(mantel_test)

export(marker)

export(matrix_data)

export(mono_mds)

export(ncols)

export(nice_curvature)

export(nrows)

export(plot_type)

export(prefix_with)

export(procrutes_test)

export(qcorrplot)

export(qpairs)

export(rand_correlate)
@@ -164,7 +121,6 @@ export(trim_diag) 
importFrom(dplyr,bind_cols)

importFrom(dplyr,bind_rows)

importFrom(dplyr,mutate)

importFrom(geomtextpath,GeomTextpath)

importFrom(ggplot2,Geom)

importFrom(ggplot2,GeomCurve)

importFrom(ggplot2,GeomPoint)
@@ -238,7 +194,6 @@ importFrom(igraph,as.igraph) 
importFrom(igraph,graph_from_data_frame)

importFrom(igraph,vertex_attr)

importFrom(magrittr,"%>%")

importFrom(purrr,map)

importFrom(purrr,map_dbl)

importFrom(purrr,pmap)

importFrom(purrr,pmap_dfr)
@@ -258,7 +213,6 @@ importFrom(stats,na.exclude) 
importFrom(stats,p.adjust)

importFrom(stats,p.adjust.methods)

importFrom(stats,runif)

importFrom(stats,setNames)

importFrom(tibble,as_tibble)

importFrom(tibble,tibble)

importFrom(tidygraph,as_tbl_graph)

R/as-correlate.R

+0 −5
Original line number Diff line number Diff line
@@ -7,14 +7,12 @@ 
#' @param ... others parameters.

#' @return a correlate object.

#' @rdname as_correlate

#' @export

as_correlate <- function(x, ...) {

  UseMethod("as_correlate")

}



#' @method as_correlate rcorr

#' @rdname as_correlate

#' @export

as_correlate.rcorr <- function(x, ...) {

  p <- x$P

  diag(p) <- 0
@@ -23,14 +21,12 @@ as_correlate.rcorr <- function(x, ...) { 


#' @method as_correlate corr.test

#' @rdname as_correlate

#' @export

as_correlate.corr.test <- function(x, ...) {

  structure(.Data = list(r = x$r, p = x$p), class = "correlate")

}



#' @method as_correlate matrix

#' @rdname as_correlate

#' @export

as_correlate.matrix <- function(x,

                                is_corr = NULL,

                                p = NULL,
@@ -55,7 +51,6 @@ as_correlate.matrix <- function(x, 


#' @method as_correlate data.frame

#' @rdname as_correlate

#' @export

as_correlate.data.frame <- function(x, ...) {

  as_correlate(as.matrix(x), ...)

}

R/as-matrix-data.R

+0 −7
Original line number Diff line number Diff line
@@ -15,7 +15,6 @@ as_matrix_data <- function(x, ...) 
}



#' @rdname as_matrix_data

#' @export

#' @method as_matrix_data matrix

as_matrix_data.matrix <- function(x,

                                  name = NULL,
@@ -32,7 +31,6 @@ as_matrix_data.matrix <- function(x, 


#' @param include one of "numeric" (default), "character" or "factor".

#' @rdname as_matrix_data

#' @export

#' @method as_matrix_data data.frame

as_matrix_data.data.frame <- function(x,

                                      name = NULL,
@@ -53,7 +51,6 @@ as_matrix_data.data.frame <- function(x, 
}



#' @rdname as_matrix_data

#' @export

#' @method as_matrix_data correlate

as_matrix_data.correlate <- function(x,

                                     extra_mat = list(),
@@ -72,7 +69,6 @@ as_matrix_data.correlate <- function(x, 
}



#' @rdname as_matrix_data

#' @export

#' @method as_matrix_data grouped_correlate

as_matrix_data.grouped_correlate <- function(x,

                                             extra_mat = list(),
@@ -95,7 +91,6 @@ as_matrix_data.grouped_correlate <- function(x, 
}



#' @rdname as_matrix_data

#' @export

#' @method as_matrix_data rcorr

as_matrix_data.rcorr <- function(x,

                                 extra_mat = list(),
@@ -105,7 +100,6 @@ as_matrix_data.rcorr <- function(x, 
}



#' @rdname as_matrix_data

#' @export

#' @method as_matrix_data corr.test

as_matrix_data.corr.test <- function(x,

                                     extra_mat = list(),
@@ -115,7 +109,6 @@ as_matrix_data.corr.test <- function(x, 
}



#' @rdname as_matrix_data

#' @export

#' @method as_matrix_data default

as_matrix_data.default <- function(x, ...)

{

R/as-md-tbl.R

+10 −34
Original line number Diff line number Diff line
@@ -21,7 +21,6 @@ as_md_tbl <- function(x, ...) { 


#' @method as_md_tbl matrix_data

#' @rdname as_md_tbl

#' @export

as_md_tbl.matrix_data <- function(x, ...)

{

  type <- attr(x, "type")
@@ -50,7 +49,6 @@ as_md_tbl.matrix_data <- function(x, ...) 


#' @method as_md_tbl grouped_matrix_data

#' @rdname as_md_tbl

#' @export

as_md_tbl.grouped_matrix_data <- function(x, ...)

{

  type <- vapply(x, attr, character(1), "type")
@@ -92,33 +90,8 @@ as_md_tbl.grouped_matrix_data <- function(x, ...) 
            class = clss)

}



#' @method as_md_tbl pro_tbl

#' @rdname as_md_tbl

#' @export

as_md_tbl.pro_tbl <- function(x, byrow = TRUE, ...) {

  class(x) <- class(x)[-1L]

  grouped <- attr(x, "grouped")

  spec <- env <- NULL

  if(isTRUE(byrow)) {

    x <- as_md_tbl(x,

                   row_vars = spec,

                   col_vars = env,

                   is_corr = TRUE)

  } else {

    x <- as_md_tbl(x,

                   row_vars = env,

                   col_vars = spec,

                   is_corr = TRUE)

  }

  if (isTRUE(grouped)) {

    class(x) <- c("cor_md_tbl", "grouped_md_tbl", "md_tbl", "tbl_df", "tbl", "data.frame")

  }

  x

}



#' @method as_md_tbl mantel_tbl

#' @rdname as_md_tbl

#' @export

as_md_tbl.mantel_tbl <- function(x, byrow = TRUE, ...) {

  class(x) <- class(x)[-1L]

  grouped <- attr(x, "grouped")
@@ -142,7 +115,6 @@ as_md_tbl.mantel_tbl <- function(x, byrow = TRUE, ...) { 


#' @method as_md_tbl easycorrelation

#' @rdname as_md_tbl

#' @export

as_md_tbl.easycorrelation <- function(x,

                                      type = "full",

                                      diag = TRUE,
@@ -228,7 +200,6 @@ as_md_tbl.easycorrelation <- function(x, 


#' @method as_md_tbl correlate

#' @rdname as_md_tbl

#' @export

as_md_tbl.correlate <- function(x, ...) {

  x <- as_md_tbl(as_matrix_data(x, ...))

  class(x) <- c("cor_md_tbl", class(x))
@@ -237,7 +208,6 @@ as_md_tbl.correlate <- function(x, ...) { 


#' @method as_md_tbl grouped_correlate

#' @rdname as_md_tbl

#' @export

as_md_tbl.grouped_correlate <- function(x, ...) {

  x <- as_md_tbl(as_matrix_data(x, ...))

  class(x) <- c("cor_md_tbl", class(x))
@@ -246,7 +216,6 @@ as_md_tbl.grouped_correlate <- function(x, ...) { 


#' @method as_md_tbl rcorr

#' @rdname as_md_tbl

#' @export

as_md_tbl.rcorr <- function(x, ...) {

  as_md_tbl(as_correlate(x), ...)

}
@@ -266,7 +235,6 @@ as_md_tbl.corr.test <- function(x, ...) { 
#' @param p_vars variable name of p value column.

#' @method as_md_tbl data.frame

#' @rdname as_md_tbl

#' @export

as_md_tbl.data.frame <- function(x,

                                 name = NULL,

                                 row_vars = NULL,
@@ -332,7 +300,6 @@ as_md_tbl.data.frame <- function(x, 


#' @method as_md_tbl matrix

#' @rdname as_md_tbl

#' @export

as_md_tbl.matrix <- function(x, ...) {

  x <- as.data.frame(x)

  as_md_tbl(x, ...)
@@ -340,8 +307,17 @@ as_md_tbl.matrix <- function(x, ...) { 


#' @method as_md_tbl md_tbl

#' @rdname as_md_tbl

#' @export

as_md_tbl.md_tbl <- function(x, ...) {

  x

}



#' @method as_md_tbl md_tbl

#' @rdname as_md_tbl

as_md_tbl.default <- function(x, ...) {

  x <- tryCatch(as.matrix(x), error = function(e) {

    msg <- paste("Cannot convert a", class(x)[1L], "object to md_tbl.")

    stop(msg, call. = FALSE)

  })

  as_md_tbl(x, ...)

}

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