diff --git a/NAMESPACE b/NAMESPACE
index ceab112..62b6d86 100644
--- 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 b/R/accuracy_test.R
similarity index 97%
rename from R/ppr_accuracy_test.R
rename to R/accuracy_test.R
index 4882e3c..ba51cea 100644
--- a/R/ppr_accuracy_test.R
+++ b/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 b/R/cell_plot.R
similarity index 99%
rename from R/ppr_cell_plot.R
rename to R/cell_plot.R
index 75c7c6a..cfdb78e 100644
--- a/R/ppr_cell_plot.R
+++ b/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
deleted file mode 100644
index 7d05332..0000000
--- a/R/ppr_racinglines_plot.R
+++ /dev/null
@@ -1,113 +0,0 @@
-#' @title Identify and Visualise each cells position.
-#'
-#' @description
-#' Produces a plot for each cell which helps visualize how PathPinPointR is predicting the cells position.
-#'
-#' @param reference.sg A selection of switching genes which are evenly distributed through pseudo-time.
-#' @param lines logical, do you want to include lines to indicate the predicted position of a cell
-#' @param reference_reduced a matrix of your sample's binary gene expression.
-#' @param cell_id The index or name of the cell of interest
-#'
-#' @return Timeline plot of selected cell
-#' @import ggplot2
-#' @import ggrepel
-#'
-#'
-#' @export
-#'
-
-ppr_timeline_plot <- function(reference.sg, lines = TRUE, reference_reduced = NULL, cell_id = 1) {
-
-  # Convert reference.sg to a data frame
-  reference.sg <- as.data.frame(reference.sg)
-
-  # Add a new column direction_num and set it to -1
-  reference.sg$direction_num <- -1
-
-  # If "up" is present in the direction column, set direction_num to 1
-  if ("up" %in% reference.sg$direction) {
-    reference.sg[reference.sg$direction == "up", ]$direction_num <- 1
-  }
-
-  # Generate pseudotime data based on the specified parameters
-    timeidx_df <- data.frame(timeidx_range = c(0, 25, 50, 75, 100), timeidx_labs = c(0, 25, 50, 75, 100))
-
-
-  # Create the initial ggplot object with x and y aesthetics, color, and labels
-  timeline_plot <- ggplot(reference.sg, aes(x = switch_at_timeidx, y = pseudoR2s * direction_num, label = rownames(reference.sg))) +
-    geom_point(size = 1) + xlab("Time-Index") + ylab("Quality of fitting (R^2)")
-
-  # Add the classic theme to the plot
-  timeline_plot <- timeline_plot + theme_classic()
-
-  # Add a horizontal black line for the timeline
-  timeline_plot <- timeline_plot + geom_hline(yintercept = 0, color = "black", linewidth = 0.6)
-
-  # Add labels for pseudotime on the plot
-  timeline_plot <- timeline_plot + geom_label(data = timeidx_df, aes(x = timeidx_range, y = 0, label = timeidx_labs),
-                                    size = (3), color = "black")
-
-  # Add text labels with repulsion to avoid overlap
-  timeline_plot <- timeline_plot + geom_text_repel(aes(x = switch_at_timeidx, y = pseudoR2s * direction_num, label = rownames(reference.sg)),
-                                         size = 3, show.legend = FALSE)
-
-  # Customize the theme and legend appearance
-  timeline_plot <- timeline_plot + theme(legend.position = "bottom", legend.title = element_blank(), legend.key.size = unit(10, "pt"),
-                               text = element_text(size = 12))
-
-
-if (lines) {
-
-  if (is.character(cell_id)) {
-    cell_idx <- which(colnames(reference_reduced) == cell_id)
-  } else if (is.numeric(cell_id)) {
-    # Convert numeric to integer if needed
-    cell_idx <- as.integer(cell_id)
-  } else {
-    stop("cell_id must be character or numeric.")
-  }
-
-  ## Reorder reference.sg
-  # as the code relies on the rownames and idicies of the genes in reference_reduced and reference.sg matching.
-  reference_reduced <- reference_reduced[rownames(reference.sg),]
-
-  # Check if row names in reference.sg match those in reference_reduced
-  if (!setequal(rownames(reference.sg), rownames(reference_reduced))) {
-    stop("Row names in reference.sg do not match those in reference_reduced")
-  }
-
-  #loop through all of the genes in reference.sg.
-    for (g in 1:dim(reference.sg)[1]) {
-      # if G is NOT expressed in  C, and the switch is UP  , then draw the line to the right.
-      if ((reference_reduced[rownames(reference.sg)[g], cell_idx] == 0) && (reference.sg$direction[g] == "up")) {
-        timeline_plot <- timeline_plot + geom_segment(aes_string(x = 0, xend = reference.sg$switch_at_timeidx[g], y = reference.sg$pseudoR2s[g], yend = reference.sg$pseudoR2s[g]),
-                                                      color = "blue", linewidth = 0.6)
-      }
-      # if G is expressed in      c, and the switch is UP  , then draw the line to the right.
-      if ((reference_reduced[rownames(reference.sg)[g], cell_idx] == 1) && (reference.sg$direction[g] == "up")) {
-        timeline_plot <- timeline_plot + geom_segment(aes_string(x = reference.sg$switch_at_timeidx[g], xend = 100, y = reference.sg$pseudoR2s[g], yend = reference.sg$pseudoR2s[g]),
-                                                      color = "blue", linewidth = 0.6)
-      }
-      # if G is NOT expressed in  C, and the switch is Down, then draw the line to the Left.
-      if ((reference_reduced[rownames(reference.sg)[g], cell_idx] == 0) && (reference.sg$direction[g] == "down")) {
-        timeline_plot <- timeline_plot + geom_segment(aes_string(x = reference.sg$switch_at_timeidx[g], xend = 100, y = -reference.sg$pseudoR2s[g], yend = -reference.sg$pseudoR2s[g]),
-                                                      color = "blue", linewidth = 0.6)
-      }
-      # if G is expressed in      C, and the switch is Down, then draw the line to the Left.
-      if ((reference_reduced[rownames(reference.sg)[g], cell_idx] == 1) && (reference.sg$direction[g] == "down")) {
-        timeline_plot <- timeline_plot + geom_segment(aes_string(x = 0, xend = reference.sg$switch_at_timeidx[g], y = -reference.sg$pseudoR2s[g], yend = -reference.sg$pseudoR2s[g]),
-                                                      color = "blue", linewidth = 0.6)
-      }
-    }
-
-# Title the plot with the name of the cell
-timeline_plot <- timeline_plot + ggtitle(colnames(reference_reduced)[cell_idx])
-
-
-}
-
-# Return the final plot
-return(timeline_plot)
-
-}
-
diff --git a/R/ppr_precision.R b/R/precision.R
similarity index 96%
rename from R/ppr_precision.R
rename to R/precision.R
index 8cbe61b..9f7c7d5 100644
--- a/R/ppr_precision.R
+++ b/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 b/R/timeline_plot.R
similarity index 99%
rename from R/ppr_timeline_plot.R
rename to R/timeline_plot.R
index 1614d99..5bc50a0 100644
--- a/R/ppr_timeline_plot.R
+++ b/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 b/R/utils.R
similarity index 100%
rename from R/ppr_utils.R
rename to R/utils.R
diff --git a/R/ppr_welcome.R b/R/welcome_to_PathPinpointR.R
similarity index 100%
rename from R/ppr_welcome.R
rename to R/welcome_to_PathPinpointR.R
diff --git a/man/PPR_OBJECT-class.Rd b/man/PPR_OBJECT-class.Rd
index 9590c34..26168b3 100644
--- a/man/PPR_OBJECT-class.Rd
+++ b/man/PPR_OBJECT-class.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_utils.R
+% Please edit documentation in R/utils.R
 \docType{class}
 \name{PPR_OBJECT-class}
 \alias{PPR_OBJECT-class}
diff --git a/man/ppr_accuracy_test.Rd b/man/ppr_accuracy_test.Rd
index 2d1760f..31ddc33 100644
--- a/man/ppr_accuracy_test.Rd
+++ b/man/ppr_accuracy_test.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_accuracy_test.R
-\name{ppr_accuracy_test}
-\alias{ppr_accuracy_test}
+% Please edit documentation in R/accuracy_test.R
+\name{accuracy_test}
+\alias{accuracy_test}
 \title{accuracy_test}
 \usage{
-ppr_accuracy_test(sample_ppr, reference_sce, plot = TRUE)
+accuracy_test(sample_ppr, reference_sce, plot = TRUE)
 }
 \arguments{
 \item{sample_ppr}{A "PPR_OBJECT" which originates from the reference,
diff --git a/man/ppr_cell_plot.Rd b/man/ppr_cell_plot.Rd
index bdc2261..fd5f9c9 100644
--- a/man/ppr_cell_plot.Rd
+++ b/man/ppr_cell_plot.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_cell_plot.R
-\name{ppr_cell_plot}
-\alias{ppr_cell_plot}
+% Please edit documentation in R/cell_plot.R
+\name{cell_plot}
+\alias{cell_plot}
 \title{PPR INDIVIDUAL CELL PLOT}
 \usage{
-ppr_cell_plot(
+cell_plot(
   sample_ppr,
   cell_idx = 1,
   col = "red",
diff --git a/man/ppr_precision.Rd b/man/ppr_precision.Rd
index 445509e..c303479 100644
--- a/man/ppr_precision.Rd
+++ b/man/ppr_precision.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_precision.R
-\name{ppr_precision}
-\alias{ppr_precision}
-\title{ppr_precision}
+% Please edit documentation in R/precision.R
+\name{precision}
+\alias{precision}
+\title{precision}
 \usage{
-ppr_precision(sce, r2_cutoff_range = seq(0, 0.5, 0.1), plot = TRUE)
+precision(sce, r2_cutoff_range = seq(0, 0.5, 0.1), plot = TRUE)
 }
 \arguments{
 \item{sce}{SingleCellExperiement object,
diff --git a/man/ppr_timeline_plot.Rd b/man/ppr_timeline_plot.Rd
index 77e3e74..b71373a 100644
--- a/man/ppr_timeline_plot.Rd
+++ b/man/ppr_timeline_plot.Rd
@@ -1,17 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_racinglines_plot.R, R/ppr_timeline_plot.R
-\name{ppr_timeline_plot}
-\alias{ppr_timeline_plot}
+% Please edit documentation in R/timeline_plot.R
+\name{timeline_plot}
+\alias{timeline_plot}
 \title{Identify and Visualise each cells position.}
 \usage{
-ppr_timeline_plot(
-  switching_genes,
-  genomic_expression_traces = FALSE,
-  reduced_sce = NULL,
-  cell_id = 1
-)
-
-ppr_timeline_plot(
+timeline_plot(
   switching_genes,
   genomic_expression_traces = FALSE,
   reduced_sce = NULL,
@@ -28,21 +21,11 @@ Do you want lines which indicate the predicted position of the selected cell.}
 that you have already run PathPinPointR::subset_switching_genes() on.}
 
 \item{cell_id}{The index or name of the cell of interest}
-
-\item{reference.sg}{A selection of switching genes which are evenly distributed through pseudo-time.}
-
-\item{lines}{logical, do you want to include lines to indicate the predicted position of a cell}
-
-\item{reference_reduced}{a matrix of your sample's binary gene expression.}
 }
 \value{
-Timeline plot of selected cell
-
 Timeline plot of selected cell
 }
 \description{
-Produces a plot for each cell which helps visualize how PathPinPointR is predicting the cells position.
-
 Produces a plot for a given cell,
 this helps visualize predicted position of the selected cell.
 }
diff --git a/man/print-PPR_OBJECT-method.Rd b/man/print-PPR_OBJECT-method.Rd
index c97a7f7..3dbff84 100644
--- a/man/print-PPR_OBJECT-method.Rd
+++ b/man/print-PPR_OBJECT-method.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_utils.R
+% Please edit documentation in R/utils.R
 \name{print,PPR_OBJECT-method}
 \alias{print,PPR_OBJECT-method}
 \title{Set Default Print Method for PPR_OBJECT}
diff --git a/man/print.PPR_OBJECT.Rd b/man/print.PPR_OBJECT.Rd
index 0c47ae7..7e1410b 100644
--- a/man/print.PPR_OBJECT.Rd
+++ b/man/print.PPR_OBJECT.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_utils.R
+% Please edit documentation in R/utils.R
 \name{print.PPR_OBJECT}
 \alias{print.PPR_OBJECT}
 \title{Print method for PPR Object.}
diff --git a/man/which_mid_max.Rd b/man/which_mid_max.Rd
index 12c556f..33645e6 100644
--- a/man/which_mid_max.Rd
+++ b/man/which_mid_max.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ppr_utils.R
+% Please edit documentation in R/utils.R
 \name{which_mid_max}
 \alias{which_mid_max}
 \title{Select the middle index among multiple occurrences of the maximum value}