Merge branch 'master' of https://github.com/camlab-bioml/taproom

.gitignore

@@ -1 +1,3 @@
 .Rproj.user
+*.Rproj
+*.Rhistory

.travis.yml

@@ -0,0 +1,2 @@
+language: r
+bioc_check: true

DESCRIPTION

@@ -3,27 +3,37 @@ 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,
   stringr,
   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

NAMESPACE

@@ -1,20 +1,28 @@
 # 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)
 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)

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",

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"))
 

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) {
 

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) {

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

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) +

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)) {