allow subseting by significance catagory

NAMESPACE

@@ -6,6 +6,7 @@ export(polar_grid)
 export(radial_ggplot)
 export(radial_plotly)
 export(show_grid)
+export(significance_subset)
 export(volcano3D)
 export(volcano_plot)
 export(volcano_trio)
@@ -47,6 +48,7 @@ importFrom(grDevices,col2rgb)
 importFrom(grDevices,hsv)
 importFrom(grDevices,rgb)
 importFrom(graphics,text)
+importFrom(methods,slot)
 importFrom(plotly,"%>%")
 importFrom(plotly,add_markers)
 importFrom(plotly,add_text)

NEWS.md

@@ -4,6 +4,7 @@ News
 # volcano3D 1.1.0
 ###### 04/02/2021
 * allow colour coding to be based on pvalue or adjusted pvalue according to cutoff_criteria
+* allow subsetting by significance groups with the significance_subset function
 
 # volcano3D 1.0.3
 ###### 15/08/2020

R/significance_subset.R

@@ -0,0 +1,59 @@
+#' Extract a subset population
+#'
+#' Subsets data according to the significance groups. 
+#' @param polar A polar object including expression data from groups of
+#' interest. Created by \code{\link{polar_coords}}.
+#' @param significance Which significance factors to subset to. If NULL 
+#' levels(syn_polar@polar$sig)[1] is selected. 
+#' @param output What object to return. Options are "pvalues", "expression", 
+#' "polar_df" for subset data frames or "polar" for subset polar class object. 
+#' @references
+#' Lewis, Myles J., et al. (2019).
+#' \href{https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31007-1}{
+#' Molecular portraits of early rheumatoid arthritis identify clinical and
+#' treatment response phenotypes.}
+#' \emph{Cell reports}, \strong{28}:9
+#' @importFrom methods slot
+#' @export
+#' @examples
+#' data(example_data)
+#' syn_polar <- polar_coords(sampledata = syn_example_meta,
+#'                           contrast = "Pathotype",
+#'                           groups = NULL,
+#'                           pvalues = syn_example_p,
+#'                           expression = syn_example_rld,
+#'                           p_col_suffix = "pvalue",
+#'                           padj_col_suffix = "padj",
+#'                           non_sig_name = "Not Significant",
+#'                           multi_group_prefix = "LRT",
+#'                           significance_cutoff = 0.01,
+#'                           fc_col_suffix='log2FoldChange',
+#'                           fc_cutoff = 0.3)
+#'
+#' subset <- significance_subset(syn_polar, "Lymphoid+", "polar_df")
+
+significance_subset <- function(polar,
+                                significance = NULL, 
+                                output = "pvalues"){
+
+  if(is.null(significance)) significance <- levels(polar@polar$sig)[1]
+  if(! all(significance %in% levels(polar@polar$sig))){
+    stop("Significance must be in levels(polar@polar$sig)")
+  }
+  if(class(polar) != "polar") stop("polar must be a polar class object")
+  if(! output %in% c("pvalues", "expression", "polar_df", "polar")){
+    stop("return must be one of 'pvalues', 'expression', 'polar_df', 'polar'")
+  }
+
+  rows <- polar@polar$Name[polar@polar$sig %in% significance]
+  polar@pvalues <- polar@pvalues[rows, ]
+  polar@expression <- polar@expression[rows, ]
+  polar@polar <- polar@polar[rows, ]
+
+  if(output == "polar"){
+    return(polar)
+  } else {
+    return(slot(polar, gsub("_df", "", output)))
+  }
+}
+