From d3da264c21384311fd0b6e2f18e9a092c5e19e6a Mon Sep 17 00:00:00 2001
From: Sam El-Kamand
Date: Mon, 5 Aug 2024 13:27:42 +1000
Subject: [PATCH 1/2] docs: data source acknowledgement and minor revisions
---
paper/jats/paper.jats | 29 ++++++++++++++++++-----------
paper/paper.bib | 34 ++++++++++++++++++++++++++--------
paper/paper.md | 11 ++++++-----
paper/paper.pdf | Bin 725422 -> 727028 bytes
4 files changed, 50 insertions(+), 24 deletions(-)
diff --git a/paper/jats/paper.jats b/paper/jats/paper.jats
index c7bef55..5597371 100644
--- a/paper/jats/paper.jats
+++ b/paper/jats/paper.jats
@@ -18,8 +18,8 @@
0
N/A
-ggoncoplot: an R package for visualising somatic mutation
-data from cancer patient cohorts
+ggoncoplot: an R package for interactive visualisation of
+somatic mutation data from cancer patient cohorts
@@ -105,9 +105,9 @@ a Creative Commons Attribution 4.0 International License (CC BY
types, including gene expression t-SNE plots or methylation UMAPs. The
simplest and most intuitive approach to examining such relations is to
link plots dynamically such that samples selected in an oncoplot can
- be highlighted in other plots. There are, however, no existing
- oncoplot-generating R packages that support dynamic data linkage
- between different plots. To address this gap and enable rapid
+ be highlighted in other plots, and vice versa. There are, however, no
+ existing oncoplot-generating R packages that support dynamic data
+ linkage between different plots. To address this gap and enable rapid
exploration of a variety of data types we constructed the ggoncoplot
package for the production of oncoplots that are easily integrated
with custom visualisations and that support synchronised
@@ -140,12 +140,16 @@ a Creative Commons Attribution 4.0 International License (CC BY
samples were automatically highlighted on the UMAP and oncoplot.
This reveals that samples which cluster on the left of the t-SNE
plot also cluster in the oncoplot, chiefly containing mutations in
- TP53 but wild type PIK3CA. The plots of progesterone, estrogen, HER2
+ TP53 and wild type PIK3CA. The plots of progesterone, estrogen, HER2
status and triple negative classification show that the samples
- selected in the t-SNE are virtually all triple negative breast
+ selected in the t-SNE are enriched for triple negative breast
cancers. In contrast to the oncoplot, the methylation UMAP shows no
- strong clustering, in line with knowledge of methylation patterns in
- triple negative breast cancer.
+ strong clustering, consistent with knowledge of methylation patterns
+ in triple negative breast cancer. Methylation, expression, and
+ genome data were originally obtained from the UCSC Xena TCGA
+ Pan-Cancer Atlas Hub [goldman:2020]. Expression and methylation
+ plots were produced with
+ express.
- Auto-colouring: Automatic selection of colour
- palettes for datasets where the consequence annotations are
+
Auto-colouring: Automatic selection of accessible
+ colour palettes for datasets where the consequence annotations are
aligned with standard variant effect dictionaries (PAVE, SO, or
MAF).
@@ -220,6 +224,9 @@ a Creative Commons Attribution 4.0 International License (CC BY