From a5d16efb5503f454f8aff9240551f826b7512f5e Mon Sep 17 00:00:00 2001
From: daniel-wells <daniel-wells@users.noreply.github.com>
Date: Tue, 28 May 2019 14:51:03 +0100
Subject: [PATCH] update docs

---
 NAMESPACE                      |  1 +
 man/genome_loadings.Rd         |  6 +++++-
 man/load_chromosome_lengths.Rd | 17 +++++++++++++++++
 man/load_gene_locations.Rd     |  2 +-
 4 files changed, 24 insertions(+), 2 deletions(-)
 create mode 100644 man/load_chromosome_lengths.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 66ff227..c1378a2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,6 +9,7 @@ export(export_data)
 export(genome_loadings)
 export(highest_components)
 export(highest_genes)
+export(load_chromosome_lengths)
 export(load_gene_locations)
 export(load_results)
 export(loading_distribution)
diff --git a/man/genome_loadings.Rd b/man/genome_loadings.Rd
index 6ce1d0c..920c912 100644
--- a/man/genome_loadings.Rd
+++ b/man/genome_loadings.Rd
@@ -6,7 +6,8 @@
 \usage{
 genome_loadings(component = NULL, max.items = 20, label.size = 3,
   label.repel = 1, label_both = TRUE, label_X = FALSE,
-  min_loading = 0.01, gene_locations = NULL, hide_unknown = FALSE,
+  min_loading = 0.01, gene_locations = NULL,
+  chromosome_lengths = NULL, hide_unknown = FALSE,
   highlight_genes = NULL, label_genes = NULL)
 }
 \arguments{
@@ -29,6 +30,9 @@ If FALSE only genes with either positive OR negative loadings will be labeled, d
 \item{gene_locations}{data.table; The output of load_gene_locations() containing the gene chromosome location coordinates,
 if not given load_gene_locations() will be called internally.}
 
+\item{chromosome_lengths}{data.table; The ouput of load_chromosome_lengths(),
+if not given load_chromosome_lengths() will be called internally.}
+
 \item{hide_unknown}{logical; if TRUE genes wihtout a chromosome (e.g. placed in scaffolds) are not plotted}
 
 \item{highlight_genes}{charachter vector of gene names; if provided, these genes will be coloured red}
diff --git a/man/load_chromosome_lengths.Rd b/man/load_chromosome_lengths.Rd
new file mode 100644
index 0000000..3be10f8
--- /dev/null
+++ b/man/load_chromosome_lengths.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotting.R
+\name{load_chromosome_lengths}
+\alias{load_chromosome_lengths}
+\title{Load chromosome lengths}
+\usage{
+load_chromosome_lengths(organism = "mmusculus_gene_ensembl")
+}
+\arguments{
+\item{organism}{character; which dataset from Ensembl should be used, e.g. "mmusculus_gene_ensembl" or "hsapiens_gene_ensembl"}
+}
+\value{
+A data table with columns: chromosome, length, length_padded, genomic_offset, center
+}
+\description{
+Load chromosome lengths
+}
diff --git a/man/load_gene_locations.Rd b/man/load_gene_locations.Rd
index 0a822b7..4e441be 100644
--- a/man/load_gene_locations.Rd
+++ b/man/load_gene_locations.Rd
@@ -19,7 +19,7 @@ load_gene_locations(genes = NULL, cache = TRUE, path = "",
 \item{name}{character; descriptive name of dataset, this will be appended to the standard cache file name when saving / loading the cache}
 }
 \value{
-A data table of genes chromosome and coordinate. An object named chromosome.lengths will also be created in the global environment.
+A data table of genes chromosome and coordinate.
 }
 \description{
 \code{load_gene_locations} Load gene coordinates from Ensembl biomart or Cached data