update docs

DESCRIPTION

@@ -7,7 +7,7 @@ Authors@R:
            family = "Dolgalev",
            role = c("aut", "cre"),
            email = "igor.dolgalev@nyumc.org")
-Description: A typical computational pipeline to process single-cell RNA sequencing (scRNA-seq) data  involves clustering of cells. Assignment of cell type labels to those clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging if you are not familiar with all the captured subpopulations or have unexpected contaminants. 'clustermole' provides a comprehensive meta collection of cell identity markers for thousands of human and mouse cell types sourced from a variety of databases as well as methods to query them.
+Description: Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.
 License: MIT + file LICENSE
 URL: https://github.com/igordot/clustermole
 BugReports: https://github.com/igordot/clustermole/issues

R/functions.R

@@ -4,6 +4,7 @@
 #' @param species Species for the appropriate gene symbol format: "hs" for human or "mm" for mouse.
 #'
 #' @return A data frame of markers with one gene per row.
+#'
 #' @import dplyr
 #' @export
 #'
@@ -31,6 +32,7 @@ clustermole_markers <- function(species = "hs") {
 #' @param species Species: "hs" for human or "mm" for mouse.
 #'
 #' @return A data frame of enrichment results with hypergeometric test p-values.
+#'
 #' @import methods
 #' @import dplyr
 #' @importFrom tibble as_tibble
@@ -87,6 +89,7 @@ clustermole_overlaps <- function(genes, species) {
 
   # clean up the enrichment table
   overlaps_tbl <- tibble::as_tibble(overlaps_mat, rownames = "celltype_full")
+  overlaps_tbl <- dplyr::filter(overlaps_tbl, .data$p_value < 0.05)
   overlaps_tbl <- dplyr::inner_join(celltypes_tbl, overlaps_tbl, by = "celltype_full")
   overlaps_tbl <- dplyr::arrange(overlaps_tbl, .data$fdr, .data$p_value, .data$celltype_full)
   overlaps_tbl
@@ -98,12 +101,16 @@ clustermole_overlaps <- function(genes, species) {
 #' @param species Species: "hs" for human or "mm" for mouse.
 #'
 #' @return A data frame of enrichment results.
+#'
 #' @import methods
 #' @import dplyr
 #' @importFrom tibble as_tibble
 #' @importFrom tidyr gather
 #' @importFrom GSVA gsva
 #' @export
+#'
+#' @examples
+#' # my_enrichment <- clustermole_enrichment(expr_mat = my_expr_mat, species = "hs")
 clustermole_enrichment <- function(expr_mat, species) {
 
   # check that the expression matrix seems reasonable
@@ -156,6 +163,7 @@ clustermole_enrichment <- function(expr_mat, species) {
 #' @param gene_label Column name for genes (variable columns of the GMT file) in the output data frame.
 #'
 #' @return A data frame with gene sets as the first column and genes as the second column (one gene per row).
+#'
 #' @import utils
 #' @importFrom tibble enframe
 #' @importFrom tidyr unnest

README.md

@@ -6,15 +6,19 @@
 
 ![clustermole-book](https://user-images.githubusercontent.com/6363505/72761156-12414280-3ba9-11ea-87de-57ff6cd690bb.png)
 
-A typical computational pipeline to process single-cell RNA sequencing (scRNA-seq) data includes clustering of cells as one of the steps. Assignment of cell type labels to those clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging for those who are not familiar with all the captured subpopulations or have unexpected contaminants. The clustermole R package provides a comprehensive meta collection of cell identity markers for thousands of human and mouse cell types sourced from a variety of databases as well as methods to query them.
+## About
+
+Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.
 
 The clustermole package provides three primary features:
 
 * cell type prediction based on marker genes
 * cell type prediction based on a full expression matrix
 * a database of cell type markers
 
----
+## Usage
+
+A [vignette](https://CRAN.R-project.org/package=clustermole/vignettes/clustermole-intro.html) is available with usage examples.
 
 Install clustermole from CRAN:
 

tests/testthat/test-functions.R

@@ -42,7 +42,7 @@ test_that("clustermole_overlaps() wrong input", {
 test_that("clustermole_overlaps() human input", {
   overlap_tbl <- clustermole_overlaps(genes = gene_names[1:50], species = "hs")
   expect_s3_class(overlap_tbl, "tbl_df")
-  expect_gt(nrow(overlap_tbl), 100)
+  expect_gt(nrow(overlap_tbl), 1)
 })
 
 # gene list for mouse overrepresentation tests
@@ -52,7 +52,7 @@ gene_names <- sample(gene_names)
 test_that("clustermole_overlaps() mouse input", {
   overlap_tbl <- clustermole_overlaps(genes = gene_names[1:50], species = "mm")
   expect_s3_class(overlap_tbl, "tbl_df")
-  expect_gt(nrow(overlap_tbl), 100)
+  expect_gt(nrow(overlap_tbl), 1)
 })
 
 # clustermole_enrichment -----

vignettes/clustermole-intro.Rmd

@@ -1,27 +1,38 @@
 ---
 title: "Introduction to clustermole"
+subtitle: "blindly digging for cell types in scRNA-seq clusters"
 output:
   prettydoc::html_pretty:
     keep_md: true
     toc: true
     theme: hpstr
     highlight: github
+    mathjax: null
+    self_contained: true
 vignette: >
   %\VignetteIndexEntry{Introduction to clustermole}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r, include=FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
 ```
 
+```{css, echo=FALSE}
+.header-title h2 {
+  text-transform: none;
+  font-style: italic;
+  font-size: 1.2rem;
+}
+```
+
 ## Overview
 
-A typical computational pipeline to process single-cell RNA sequencing (scRNA-seq) data includes clustering of cells as one of the steps. Assignment of cell type labels to those clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging for those who are not familiar with all the captured subpopulations or have unexpected contaminants. The clustermole R package provides a comprehensive meta collection of cell identity markers for thousands of human and mouse cell types sourced from a variety of databases as well as methods to query them.
+A typical computational pipeline to process single-cell RNA sequencing (scRNA-seq) data includes clustering of cells as one of the steps. Assignment of cell type labels to those clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.
 
 The clustermole package provides three primary features:
 
@@ -78,15 +89,15 @@ If you need to convert the markers from a data frame to a list format for other
 markers_list = split(x = markers$gene, f = markers$celltype_full)
 ```
 
-## Collection details
+## Database details
 
 We will load dplyr to help with the summary statistics.
 
 ```{r load-dplyr, message=FALSE}
 library(dplyr)
 ```
 
-You can use `clustermole_markers()` to retrieve a data frame of all cell type markers in the database.
+You can use `clustermole_markers()` to retrieve a data frame of all cell type markers in the collection.
 
 ```{r get-markers}
 markers = clustermole_markers(species = "hs")