Name updates

moi-taiga · Jun 24, 2024 · 9d62db8 · 9d62db8
1 parent 3f49f47
commit 9d62db8
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Showing 16 changed files with 31 additions and 163 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,17 +3,15 @@
 export(calculate_variance)
 export(calculate_zscore)
 export(plot_position)
-export(ppr_accuracy_test)
-export(ppr_cell_plot)
-export(ppr_precision)
-export(ppr_timeline_plot)
+export(accuracy_test)
+export(cell_plot)
+export(precision)
+export(timeline_plot)
 export(predict_position)
 export(print.PPR_OBJECT)
 export(subset_switching_genes)
 export(which_mid_max)
 exportClasses(PPR_OBJECT)
-import(ggplot2)
-import(ggrepel)
 importFrom(GeneSwitches,filter_switchgenes)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)

diff --git a/R/ppr_accuracy_test.R → R/accuracy_test.R b/R/ppr_accuracy_test.R → R/accuracy_test.R
@@ -15,7 +15,7 @@
 #' If plot = TRUE, returns a the accuracy data frame.
 #' @importFrom graphics abline hist text
 #' @export
-ppr_accuracy_test <- function(sample_ppr, reference_sce, plot = TRUE) {
+accuracy_test <- function(sample_ppr, reference_sce, plot = TRUE) {
   # Create a data frame to store the accuracy results
   accuracy <- data.frame(
     # Cell names from reference_sce

diff --git a/R/ppr_cell_plot.R → R/cell_plot.R b/R/ppr_cell_plot.R → R/cell_plot.R
@@ -16,7 +16,7 @@
 #' @importFrom graphics segments text lines
 #' @export
 #'
-ppr_cell_plot <- function(sample_ppr,
+cell_plot <- function(sample_ppr,
                           cell_idx = 1,
                           col = "red",
                           overlay = FALSE,

diff --git a/R/ppr_racinglines_plot.R b/R/ppr_racinglines_plot.R
diff --git a/R/ppr_precision.R → R/precision.R b/R/ppr_precision.R → R/precision.R
@@ -1,4 +1,4 @@
-#' ppr_precision
+#' precision
 #'
 #' @description
 #' Used to find the optimum r2cutoff to use,
@@ -15,7 +15,7 @@
 #' 
 #'
 #' @export
-ppr_precision <- function(sce,
+precision <- function(sce,
                           r2_cutoff_range = seq(0.0, 0.5, 0.1),
                           plot = TRUE) {
 
@@ -58,7 +58,7 @@ ppr_precision <- function(sce,
     sample_ppr <- predict_position(sample_reduced, switching_genes)
 
     #
-    accuracy <- ppr_accuracy_test(sample_ppr = sample_ppr,
+    accuracy <- accuracy_test(sample_ppr = sample_ppr,
                                   reference_sce = sce, plot = FALSE)
 
     #

diff --git a/R/ppr_timeline_plot.R → R/timeline_plot.R b/R/ppr_timeline_plot.R → R/timeline_plot.R
@@ -17,7 +17,7 @@
 #'
 #'
 #' @export
-ppr_timeline_plot <- function(switching_genes,
+timeline_plot <- function(switching_genes,
                               genomic_expression_traces = FALSE,
                               reduced_sce = NULL,
                               cell_id = 1) {

diff --git a/R/ppr_utils.R → R/utils.R b/R/ppr_utils.R → R/utils.R
diff --git a/R/ppr_welcome.R → R/welcome_to_PathPinpointR.R b/R/ppr_welcome.R → R/welcome_to_PathPinpointR.R
diff --git a/man/PPR_OBJECT-class.Rd b/man/PPR_OBJECT-class.Rd
diff --git a/man/ppr_accuracy_test.Rd b/man/ppr_accuracy_test.Rd
diff --git a/man/ppr_cell_plot.Rd b/man/ppr_cell_plot.Rd
diff --git a/man/ppr_precision.Rd b/man/ppr_precision.Rd
diff --git a/man/ppr_timeline_plot.Rd b/man/ppr_timeline_plot.Rd
diff --git a/man/print-PPR_OBJECT-method.Rd b/man/print-PPR_OBJECT-method.Rd
diff --git a/man/print.PPR_OBJECT.Rd b/man/print.PPR_OBJECT.Rd
diff --git a/man/which_mid_max.Rd b/man/which_mid_max.Rd