🆕 Add show_groups

NAMESPACE

@@ -43,6 +43,7 @@ export(show_cn_profile)
 export(show_cosmic_sig_profile)
 export(show_group_comparison)
 export(show_group_mapping)
+export(show_groups)
 export(show_sig_bootstrap_error)
 export(show_sig_bootstrap_exposure)
 export(show_sig_bootstrap_stability)

NEWS.md

@@ -1,5 +1,6 @@
 # sigminer 1.0.6
 
+- Added `show_groups()` to show the signature contribution in each group from `get_groups()`.
 - Expanded clustering in `get_groups()` to result of `sig_fit()`.
 - Properly handled null-count samples in `sig_fit_bootstrap_batch()`.
 - Added strand bias labeling for INDEL.

R/get_groups.R

@@ -51,7 +51,7 @@
 #' # Use k-means clustering
 #' get_groups(sig, method = "k-means")
 #' }
-#' @seealso [NMF::predict()]
+#' @seealso [NMF::predict()], [show_groups].
 get_groups <- function(Signature,
                        method = c("consensus", "k-means", "exposure", "samples"),
                        n_cluster = NULL,

R/show_groups.R

@@ -0,0 +1,17 @@
+#' Show Signature Contribution in Clusters
+#'
+#' See example section in [sig_fit()] for an examples.
+#'
+#' @param grp_dt a result `data.table` from [get_groups].
+#' @param ... parameters passing to [legend()], e.g. `x = "topleft"`.
+#'
+#' @return nothing.
+#' @export
+#' @seealso [get_groups], [sig_fit].
+show_groups <- function(grp_dt, ...) {
+  x2 <- attr(grp_dt, "map_table")
+  if (is.null(x2)) {
+    send_stop("Wrong input, should be result from 'get_groups'.")
+  }
+  barplot(t(x2), legend.text = TRUE, args.legend = list(...))
+}

R/sig_fit.R

@@ -51,6 +51,10 @@
 #'   H_infer
 #'   H
 #'
+#'   ## Get clusters/groups
+#'   z <- get_groups(H_infer, method = "k-means")
+#'   show_groups(z)
+#'
 #'   H_dt <- sig_fit(V, W, return_class = "data.table")
 #'   H_dt
 #'

tests/testthat/test-roxytest-testexamples-sig_fit.R

@@ -2,7 +2,7 @@
 
 context("File R/sig_fit.R: @testexamples")
 
-test_that("Function sig_fit() @ L93", {
+test_that("Function sig_fit() @ L97", {
 
   W <- matrix(c(1, 2, 3, 4, 5, 6), ncol = 2)
   colnames(W) <- c("sig1", "sig2")
@@ -19,6 +19,10 @@ test_that("Function sig_fit() @ L93", {
     H_infer
     H
 
+    ## Get clusters/groups
+    z <- get_groups(H_infer, method = "k-means")
+    show_groups(z)
+
     H_dt <- sig_fit(V, W, return_class = "data.table")
     H_dt