Add b in x3ptools::x3p_average as parameter

YuhangTom · Sep 24, 2023 · b29623b · b29623b
1 parent 0c2ecca
commit b29623b
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Showing 18 changed files with 45 additions and 37 deletions.
diff --git a/R/df_rmtrend_x3p.R b/R/df_rmtrend_x3p.R
@@ -12,7 +12,7 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #'
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_nomiss_res

diff --git a/R/vec_align_sigs_list.R b/R/vec_align_sigs_list.R
@@ -18,10 +18,10 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
-#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#' concavity = concavity, b = 1, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
 #'
 #' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
 #' vec_align_sigs_list(x3p_raw_sig_vec(x3p_bin_rotate), x3p_shift_sig_vec(x3p_bin_rotate),

diff --git a/R/x3p_MLE_angle_vec.R b/R/x3p_MLE_angle_vec.R
@@ -18,10 +18,10 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
-#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#' concavity = concavity, b = 1, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
 #'
 #' x3p_MLE_angle_vec(x3p_inner_impute, min_score_cut = 0.1, ifplot = TRUE)
 #'

diff --git a/R/x3p_impute.R b/R/x3p_impute.R
@@ -5,6 +5,7 @@
 #' @param x3p_mask x3p object for mask
 #' @param mask_col colour for the polygon
 #' @param concavity strictly positive value used in \code{concaveman::concaveman}
+#' @param b positive integer value, block size, used in \code{x3ptools::x3p_average}
 #' @param ifsave whether the imputation procedure gif is going to be saved
 #' @param dir_name required when \code{ifsave} is \code{TRUE}
 #' @param ifplot whether graphs are displayed
@@ -24,19 +25,20 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #'
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
-#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
+#' concavity = concavity, b = 1, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
 #' x3p_inner_impute
 #'
 #' if (interactive()) {
 #'   x3p_image_autosize(x3p_inner_impute)
 #' }
 #'
 x3p_impute <- function(x3p, x3p_mask, mask_col = "#FF0000",
-                       concavity = 1.5, ifsave = FALSE, dir_name = NULL, ifplot = FALSE) {
+                       concavity = 1.5, b = 10,
+                       ifsave = FALSE, dir_name = NULL, ifplot = FALSE) {
   layer <-
     x <-
     y <-
@@ -170,7 +172,7 @@ x3p_impute <- function(x3p, x3p_mask, mask_col = "#FF0000",
     x3p_surface_polygon(colour = mask_col, concavity = concavity)
   ### Extract inner part as x3p based on mask
   x3p_inner <- x3p_extract(x3p_mask, mask_vals = mask_col) %>%
-    x3p_average(b = 1, na.rm = TRUE)
+    x3p_average(b = b, na.rm = TRUE)
   x3p_inner_focal_impute <- x3p_add_mask(x3p_inner_focal_impute, x3p_inner$mask)
 
   x3p_inner_impute <- x3p_inner_focal_impute %>%

diff --git a/R/x3p_insidepoly_df.R b/R/x3p_insidepoly_df.R
@@ -4,6 +4,7 @@
 #' @param x3p x3p object
 #' @param mask_col colour for the polygon
 #' @param concavity strictly positive value used in \code{concaveman::concaveman}
+#' @param b positive integer value, block size, used in \code{x3ptools::x3p_average}
 #' @return data frame of inside polygon
 #' @import dplyr
 #' @importFrom x3ptools x3p_extract x3p_average x3p_to_df
@@ -17,10 +18,10 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' str(insidepoly_df)
 #'
-x3p_insidepoly_df <- function(x3p, mask_col = "#FF0000", concavity = 1.5) {
+x3p_insidepoly_df <- function(x3p, mask_col = "#FF0000", concavity = 1.5, b = 10) {
   to <-
     from <-
     neighbor_val <-
@@ -35,7 +36,7 @@ x3p_insidepoly_df <- function(x3p, mask_col = "#FF0000", concavity = 1.5) {
 
   ### Extract inner part as x3p based on mask
   x3p_inner <- x3p_extract(x3p, mask_vals = mask_col) %>%
-    x3p_average(b = 1, na.rm = TRUE)
+    x3p_average(b = b, na.rm = TRUE)
 
   x3p_inner_df <- x3p_inner %>%
     x3p_to_df()

diff --git a/R/x3p_quantile_angle_vec.R b/R/x3p_quantile_angle_vec.R
@@ -17,10 +17,10 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
-#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#' concavity = concavity, b = 1, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
 #'
 #' x3p_quantile_angle_vec(x3p_inner_impute, min_score_cut = 0.1, ifplot = TRUE)
 #'

diff --git a/R/x3p_raw_sig_vec.R b/R/x3p_raw_sig_vec.R
@@ -15,10 +15,10 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
-#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#' concavity = concavity, b = 1, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
 #'
 #' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
 #' x3p_raw_sig_vec(x3p_bin_rotate, ifplot = TRUE) %>%

diff --git a/R/x3p_shift_sig_vec.R b/R/x3p_shift_sig_vec.R
@@ -18,10 +18,10 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
-#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#' concavity = concavity, b = 1, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
 #'
 #' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
 #' if (interactive()) {

diff --git a/R/x3p_vertical.R b/R/x3p_vertical.R
@@ -17,10 +17,10 @@
 #' mask_col <- "#FF0000"
 #' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
-#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#' concavity = concavity, b = 1, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
 #'
 #' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1, ifplot = TRUE)
 #' x3p_bin_rotate

diff --git a/man/df_rmtrend_x3p.Rd b/man/df_rmtrend_x3p.Rd
diff --git a/man/vec_align_sigs_list.Rd b/man/vec_align_sigs_list.Rd
diff --git a/man/x3p_MLE_angle_vec.Rd b/man/x3p_MLE_angle_vec.Rd
diff --git a/man/x3p_impute.Rd b/man/x3p_impute.Rd
diff --git a/man/x3p_insidepoly_df.Rd b/man/x3p_insidepoly_df.Rd
diff --git a/man/x3p_quantile_angle_vec.Rd b/man/x3p_quantile_angle_vec.Rd
diff --git a/man/x3p_raw_sig_vec.Rd b/man/x3p_raw_sig_vec.Rd
diff --git a/man/x3p_shift_sig_vec.Rd b/man/x3p_shift_sig_vec.Rd
diff --git a/man/x3p_vertical.Rd b/man/x3p_vertical.Rd