diff --git a/.gitignore b/.gitignore
index cd67eac..a619a9b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,3 @@
 .Rproj.user
+*.Rproj
+*.Rhistory
\ No newline at end of file
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..f73dfc2
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,2 @@
+language: r
+bioc_check: true
diff --git a/DESCRIPTION b/DESCRIPTION
index 7c94981..c1d3133 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,19 +3,18 @@ Title: Tools for spAtial PROteOmics
 Version: 0.1.0
 Depends: R (>= 3.6)
 Authors@R: 
-    person(given = "First",
-           family = "Last",
+    person(given = "Ehsan",
+           family = "Karimiara",
            role = c("aut", "cre"),
-           email = "first.last@example.com",
+           email = "e.karimiara@gmail.com",
            comment = c(ORCID = "YOUR-ORCID-ID"))
 Description: What the package does (one paragraph).
-License: What license it uses
+License: file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports:
   yaml,
   scater,
-  SingleCellExperiment,
   BiocGenerics,
   SummarizedExperiment,
   plyr,
@@ -23,7 +22,18 @@ Imports:
   MASS,
   broom,
   dplyr,
-  tibble
+  tibble,
+  utils,
+  cowplot,
+  stats,
+  viridis,
+  ComplexHeatmap,
+  ggplot2,
+  wesanderson,
 Suggests:
-  crayon
-RoxygenNote: 7.1.0
+    crayon,
+    knitr,
+    rmarkdown
+RoxygenNote: 7.1.1
+biocViews: Proteomics, CellBiology, Software
+VignetteBuilder: knitr
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..e69de29
diff --git a/NAMESPACE b/NAMESPACE
index 88497b9..001733f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,9 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
+export(astir_paper_theme)
+export(cohort_colours)
+export(createHeatmap)
 export(get_celltypes)
 export(imc_exclusive_marker_score)
 export(jackson_basel_colours)
 export(patient_clinSubtype_colours)
+export(patient_clinSubtype_colours_wagner)
 export(patient_response_colours)
 export(plotSpatial)
 export(print_marker_info)
@@ -11,10 +15,14 @@ export(read_markers)
 export(tidy_rownames_jackson)
 export(to_csv)
 export(winsorize)
+import(cowplot)
+import(ggplot2)
 importFrom(BiocGenerics,rownames)
 importFrom(ComplexHeatmap,Heatmap)
 importFrom(ComplexHeatmap,HeatmapAnnotation)
 importFrom(MASS,rlm)
+importFrom(SummarizedExperiment,"assay<-")
+importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
 importFrom(broom,tidy)
@@ -24,9 +32,12 @@ importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(plyr,mapvalues)
 importFrom(scater,plotColData)
+importFrom(stats,quantile)
 importFrom(stringr,str_locate)
 importFrom(stringr,str_sub)
 importFrom(tibble,tibble)
 importFrom(utils,data)
+importFrom(utils,write.csv)
 importFrom(viridis,viridis)
+importFrom(wesanderson,wes_palette)
 importFrom(yaml,read_yaml)
diff --git a/R/cleaning.R b/R/cleaning.R
index 29aa0f2..6e36789 100644
--- a/R/cleaning.R
+++ b/R/cleaning.R
@@ -9,11 +9,13 @@
 #' @param sce An input \code{SummarizedExperiment} or \code{SingleCellExperiment}
 #' @param marker_1 The name of the first marker (normally keratin)
 #' @param marker_2 The name of the second marker (normally CD45/PTPRC)
+#' @param assay_name Type of SingleCellExperiment
 #'
 #' @importFrom MASS rlm
 #' @importFrom SummarizedExperiment assay
 #' @importFrom broom tidy
 #'
+#' @examples counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 imc_exclusive_marker_score <- function(sce,
                                        marker_1 = "pan Cytokeratin",
diff --git a/R/colours.R b/R/colours.R
index dcba3dd..1495a78 100644
--- a/R/colours.R
+++ b/R/colours.R
@@ -1,5 +1,6 @@
 
 #' Celltype colours for Jackson Basel 2020
+#' @examples colors <-jackson_basel_colours()
 #' @export
 jackson_basel_colours <- function() {
   pal <- c("#8B5B42", "#AF4EA9", "#FFB60A", "#0AC694", "#0024DD", "#6CC1FF",
@@ -28,6 +29,9 @@ jackson_basel_colours <- function() {
   celltype_colours
 }
 
+#' Color maps of patient clinical subtypes
+#'
+#' @examples patient_clinSubtype_colours()
 #' @export
 patient_clinSubtype_colours <- function(){
   pal <- c("#648FFF", "#785EF0", "#DC267F", "#FE6100", "#FFB000")
@@ -41,6 +45,8 @@ patient_clinSubtype_colours <- function(){
   clinSubtype_colours
 }
 
+#' Set Wagner colour maps to patient clinical subtypes
+#' @examples patient_clinSubtype_colours_wagner()
 #' @export
 patient_clinSubtype_colours_wagner <- function(){
   pal <- c("#648FFF", "#785EF0", "#DC267F", "#FE6100", "#FFB000")
@@ -55,6 +61,8 @@ patient_clinSubtype_colours_wagner <- function(){
   clinSubtype_colours
 }
 
+#' Colour maps of patient responses
+#' @examples patient_response_colours()
 #' @export
 patient_response_colours <- function(){
   pal <- c("#648FFF", "#785EF0", "#DC267F", "#FE6100", "#FFB000")
@@ -67,7 +75,10 @@ patient_response_colours <- function(){
   clinSubtype_colours
 }
 
-#' @export
+#' Group colors
+#' @importFrom wesanderson wes_palette
+#' @examples counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+#' @export 
 cohort_colours <- function(){
   pal <- wes_palette("Darjeeling2", 4, type = c("discrete"))
   
diff --git a/R/jackson.R b/R/jackson.R
index 047e7b5..347a94b 100644
--- a/R/jackson.R
+++ b/R/jackson.R
@@ -12,6 +12,7 @@
 #' @importFrom dplyr left_join mutate case_when filter
 #' @importFrom tibble tibble
 #'
+#' @examples  counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 tidy_rownames_jackson <- function(sce) {
 
diff --git a/R/markers.R b/R/markers.R
index 378a42a..46bbd13 100644
--- a/R/markers.R
+++ b/R/markers.R
@@ -4,6 +4,8 @@
 #' 
 #' @param path Input file path (yaml file)
 #' 
+#' @examples 
+#'         counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 #' 
 #' @return A marker list including cell type and state markers
@@ -37,6 +39,8 @@ read_markers <- function(path) {
 #' 
 #' @return Prints marker information
 #' 
+#' @examples 
+#'         counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 #' 
 print_marker_info <- function(markers) {
diff --git a/R/plotting.R b/R/plotting.R
index 45f8f38..eefd097 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -6,11 +6,17 @@
 #' @param colour_by Either a feature name or column of \code{colData(sce)}
 #' @param x_str The column of \code{colData(sce)} that codes for the x coordinate
 #' @param y_str The column of \code{colData(sce)} that codes for the Y coordinate
+#' @param winsorize IDK ????
+#' @param w_limits Range of probabilities to use in quantile()
+#' @param exprs_values Type of SingleCellExperiment
 #' @param ... Additional arguments to pass to \code{plotColData}
 #'
 #' @importFrom scater plotColData
-#' @importFrom SummarizedExperiment colData
-#'
+#' @importFrom SummarizedExperiment assay colData colData<-
+#' @importFrom stats quantile
+#' 
+#' @examples 
+#'         counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 plotSpatial <- function(sce,
                         colour_by = NULL,
@@ -61,7 +67,9 @@ plotSpatial <- function(sce,
 #' @param thresh The threshold to winsorize expression values at
 #' 
 #' @return A heatmap of class \code{ComplexHeatmap::Heatmap}
-#'
+#' 
+#' @examples 
+#'         counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 #' 
 #' @importFrom SummarizedExperiment assay colData
diff --git a/R/theme.R b/R/theme.R
index b3e90b6..c054b2a 100644
--- a/R/theme.R
+++ b/R/theme.R
@@ -1,4 +1,8 @@
 #' Create a theme for all plot for the astir paper
+#' 
+#' @import cowplot
+#' @import ggplot2
+#' @examples astir_paper_theme()
 #' @export
 astir_paper_theme <- function() {
   cowplot::theme_cowplot(font_size = 12) +
diff --git a/R/utils.R b/R/utils.R
index bc78e0d..e295291 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -12,7 +12,12 @@ winsorize_one <- function(y,
 }
 
 #' Winsorize the (log) counts
+#' @param sce An input \code{SummarizedExperiment} or \code{SingleCellExperiment}
+#' @param exprs_values Type of input?
+#' @param w_limits cut off limits?
+#' @importFrom SummarizedExperiment assay<- assay
 #'
+#' @examples counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 winsorize <- function(sce,
                       exprs_values = "logcounts",
@@ -40,7 +45,11 @@ winsorize <- function(sce,
 #' @param file The output file to write to
 #' @param include_xy Logical: should spatial location be written as first two
 #' columns?
-#'
+#' @param exprs_values The type of the SingleCellExperiment?
+#' 
+#' @importFrom utils write.csv
+#' 
+#' @examples counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 to_csv <- function(sce,
                    file,
@@ -64,7 +73,10 @@ to_csv <- function(sce,
 }
 
 #' Get cell type assignments given probability matrix
+#' @param prob_mat A probability matrix?
+#' @param thresh A measure for cell type assignment?
 #'
+#' @examples counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
 #' @export
 get_celltypes <- function(prob_mat, thresh = 0.5) {
   if(is.data.frame(prob_mat)) {
diff --git a/man/astir_paper_theme.Rd b/man/astir_paper_theme.Rd
new file mode 100644
index 0000000..01f1822
--- /dev/null
+++ b/man/astir_paper_theme.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/theme.R
+\name{astir_paper_theme}
+\alias{astir_paper_theme}
+\title{Create a theme for all plot for the astir paper}
+\usage{
+astir_paper_theme()
+}
+\description{
+Create a theme for all plot for the astir paper
+}
+\examples{
+astir_paper_theme()
+}
diff --git a/man/cohort_colours.Rd b/man/cohort_colours.Rd
new file mode 100644
index 0000000..4678f14
--- /dev/null
+++ b/man/cohort_colours.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/colours.R
+\name{cohort_colours}
+\alias{cohort_colours}
+\title{Group colors}
+\usage{
+cohort_colours()
+}
+\description{
+Group colors
+}
+\examples{
+counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/createHeatmap.Rd b/man/createHeatmap.Rd
index b1c3520..ffa23f6 100644
--- a/man/createHeatmap.Rd
+++ b/man/createHeatmap.Rd
@@ -28,3 +28,6 @@ A heatmap of class \code{ComplexHeatmap::Heatmap}
 Note that this creates a \code{Heatmap} object. To plot,
 call \code{draw(...)} on the returned object.
 }
+\examples{
+        counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/get_celltypes.Rd b/man/get_celltypes.Rd
index 707ff31..0e0650d 100644
--- a/man/get_celltypes.Rd
+++ b/man/get_celltypes.Rd
@@ -6,6 +6,14 @@
 \usage{
 get_celltypes(prob_mat, thresh = 0.7)
 }
+\arguments{
+\item{prob_mat}{A probability matrix?}
+
+\item{thresh}{A measure for cell type assignment?}
+}
 \description{
 Get cell type assignments given probability matrix
 }
+\examples{
+counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/imc_exclusive_marker_score.Rd b/man/imc_exclusive_marker_score.Rd
index 6c0b3e2..40e66f9 100644
--- a/man/imc_exclusive_marker_score.Rd
+++ b/man/imc_exclusive_marker_score.Rd
@@ -17,6 +17,8 @@ imc_exclusive_marker_score(
 \item{marker_1}{The name of the first marker (normally keratin)}
 
 \item{marker_2}{The name of the second marker (normally CD45/PTPRC)}
+
+\item{assay_name}{Type of SingleCellExperiment}
 }
 \description{
 Implements a very basic QC test: CD45 and keratin should exhibit mutually
@@ -24,3 +26,6 @@ exclusive expression, so performs a robust regression to check this trend,
 and reports the z-statistic. The more negative this is, the better the
 mutually-exclusive expression (to a first approximation).
 }
+\examples{
+counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/jackson_basel_colours.Rd b/man/jackson_basel_colours.Rd
index 6f7b0b2..f45822b 100644
--- a/man/jackson_basel_colours.Rd
+++ b/man/jackson_basel_colours.Rd
@@ -9,3 +9,6 @@ jackson_basel_colours()
 \description{
 Celltype colours for Jackson Basel 2020
 }
+\examples{
+colors <-jackson_basel_colours()
+}
diff --git a/man/patient_clinSubtype_colours.Rd b/man/patient_clinSubtype_colours.Rd
new file mode 100644
index 0000000..fe74f3a
--- /dev/null
+++ b/man/patient_clinSubtype_colours.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/colours.R
+\name{patient_clinSubtype_colours}
+\alias{patient_clinSubtype_colours}
+\title{Color maps of patient clinical subtypes}
+\usage{
+patient_clinSubtype_colours()
+}
+\description{
+Color maps of patient clinical subtypes
+}
+\examples{
+patient_clinSubtype_colours()
+}
diff --git a/man/patient_clinSubtype_colours_wagner.Rd b/man/patient_clinSubtype_colours_wagner.Rd
new file mode 100644
index 0000000..11363a2
--- /dev/null
+++ b/man/patient_clinSubtype_colours_wagner.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/colours.R
+\name{patient_clinSubtype_colours_wagner}
+\alias{patient_clinSubtype_colours_wagner}
+\title{Set Wagner colour maps to patient clinical subtypes}
+\usage{
+patient_clinSubtype_colours_wagner()
+}
+\description{
+Set Wagner colour maps to patient clinical subtypes
+}
+\examples{
+patient_clinSubtype_colours_wagner()
+}
diff --git a/man/patient_response_colours.Rd b/man/patient_response_colours.Rd
new file mode 100644
index 0000000..e1902a7
--- /dev/null
+++ b/man/patient_response_colours.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/colours.R
+\name{patient_response_colours}
+\alias{patient_response_colours}
+\title{Colour maps of patient responses}
+\usage{
+patient_response_colours()
+}
+\description{
+Colour maps of patient responses
+}
+\examples{
+patient_response_colours()
+}
diff --git a/man/plotSpatial.Rd b/man/plotSpatial.Rd
index 1c8706b..b3ab09c 100644
--- a/man/plotSpatial.Rd
+++ b/man/plotSpatial.Rd
@@ -24,8 +24,17 @@ plotSpatial(
 
 \item{y_str}{The column of \code{colData(sce)} that codes for the Y coordinate}
 
+\item{winsorize}{IDK ????}
+
+\item{w_limits}{Range of probabilities to use in quantile()}
+
+\item{exprs_values}{Type of SingleCellExperiment}
+
 \item{...}{Additional arguments to pass to \code{plotColData}}
 }
 \description{
 Plot the spatial variation in gene expression or colData
 }
+\examples{
+        counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/print_marker_info.Rd b/man/print_marker_info.Rd
index ae0f187..0aa10a9 100644
--- a/man/print_marker_info.Rd
+++ b/man/print_marker_info.Rd
@@ -15,3 +15,6 @@ Prints marker information
 \description{
 Print cell type and cell state marker info
 }
+\examples{
+        counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/read_markers.Rd b/man/read_markers.Rd
index 63cb8d0..7a4075a 100644
--- a/man/read_markers.Rd
+++ b/man/read_markers.Rd
@@ -15,3 +15,6 @@ A marker list including cell type and state markers
 \description{
 Read a marker yaml file
 }
+\examples{
+        counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/tidy_rownames_jackson.Rd b/man/tidy_rownames_jackson.Rd
index 9a27135..b183b0d 100644
--- a/man/tidy_rownames_jackson.Rd
+++ b/man/tidy_rownames_jackson.Rd
@@ -12,3 +12,6 @@ tidy_rownames_jackson(sce)
 \description{
 Convert from original SC_Dat.csv rownames to understandable ones
 }
+\examples{
+ counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/to_csv.Rd b/man/to_csv.Rd
index f324d68..d22aa8c 100644
--- a/man/to_csv.Rd
+++ b/man/to_csv.Rd
@@ -24,8 +24,13 @@ columns?}
 \item{x_str}{The column of \code{colData(sce)} that codes for the x coordinate}
 
 \item{y_str}{The column of \code{colData(sce)} that codes for the Y coordinate}
+
+\item{exprs_values}{The type of the SingleCellExperiment?}
 }
 \description{
 Writes the cell names as row names, and the (X,Y) co-ordinates
 as the first two columns (named \code{X} and \code{Y}).
 }
+\examples{
+counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/man/winsorize.Rd b/man/winsorize.Rd
index 8011636..e6e3803 100644
--- a/man/winsorize.Rd
+++ b/man/winsorize.Rd
@@ -6,6 +6,16 @@
 \usage{
 winsorize(sce, exprs_values = "logcounts", w_limits = c(0.05, 0.95))
 }
+\arguments{
+\item{sce}{An input \code{SummarizedExperiment} or \code{SingleCellExperiment}}
+
+\item{exprs_values}{Type of input?}
+
+\item{w_limits}{cut off limits?}
+}
 \description{
 Winsorize the (log) counts
 }
+\examples{
+counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
+}
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000..097b241
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/taproom.Rmd b/vignettes/taproom.Rmd
new file mode 100644
index 0000000..accd64f
--- /dev/null
+++ b/vignettes/taproom.Rmd
@@ -0,0 +1,19 @@
+---
+title: "taproom"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{taproom}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(taproom)
+```