Back

scatterHatch: an R/Bioconductor package for colorblind accessible visualization of single-cell data

Guha, T.; Fertig, E.; Deshpande, A.

2021-10-07 bioinformatics
10.1101/2021.10.07.463279 bioRxiv
Show abstract

Reduced-dimension or spatial in situ scatter plots are widely employed in bioinformatics papers analyzing single-cell data to present phenomena or cell-conditions of interest in cell groups. When displaying these cell groups, color is frequently the only graphical cue used to differentiate them. However, as the complexity of the information presented in these visualizations increases, the usefulness of color as the only visual cue declines, especially for the sizable readership with color-vision deficiencies (CVDs). In this paper, we present scatterHatch, an R package that creates easily interpretable scatter plots by redundant coding of cell groups using colors as well as patterns. We give examples to demonstrate how the scatterHatch plots are more accessible than simple scatter plots when simulated for various types of CVDs.

Matching journals

The top 7 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 1%
18.9%
Similar papers in this journal
2
BMC Bioinformatics
○ 457 papers in training set
Top 0.7%
9.9%
Similar papers in this journal
3
Scientific Reports
○ 3612 papers in training set
Top 14%
5.7%
Similar papers in this journal
4
Bioinformatics Advances
◐ 203 papers in training set
Top 0.9%
5.7%
Similar papers in this journal
5
PLOS ONE
● 5266 papers in training set
Top 28%
5.3%
Similar papers in this journal
6
Biological Imaging
◐ 15 papers in training set
Top 0.1%
3.3%
7
PLOS Computational Biology
● 1863 papers in training set
Top 10%
3.3%
50% of probability mass above
8
Frontiers in Bioinformatics
○ 49 papers in training set
Top 0.2%
2.4%
9
GigaScience
◐ 212 papers in training set
Top 2%
2.4%
10
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 2%
2.4%
11
Journal of Open Source Software
● 25 papers in training set
Top 0.1%
2.4%
12
Briefings in Bioinformatics
◐ 354 papers in training set
Top 4%
2.2%
13
SoftwareX
○ 15 papers in training set
Top 0.1%
2.2%
14
Patterns
○ 78 papers in training set
Top 0.9%
2.2%
15
Journal of Microscopy
○ 20 papers in training set
Top 0.1%
2.0%
16
PeerJ
◐ 308 papers in training set
Top 4%
2.0%
17
Methods in Ecology and Evolution
○ 176 papers in training set
Top 1%
1.7%
18
iScience
○ 1154 papers in training set
Top 21%
1.5%
19
iMeta
○ 10 papers in training set
Top 0.1%
1.4%
20
STAR Protocols
○ 18 papers in training set
Top 0.2%
1.2%
21
Nature Protocols
○ 33 papers in training set
Top 0.4%
1.2%
22
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 3%
1.2%
23
Nucleic Acids Research
◐ 1281 papers in training set
Top 11%
1.1%
24
Nature Communications
○ 5641 papers in training set
Top 52%
1.1%
25
npj Systems Biology and Applications
○ 125 papers in training set
Top 2%
0.9%
26
Protein Science
○ 246 papers in training set
Top 3%
0.9%
27
eLife
● 5828 papers in training set
Top 65%
0.9%
28
Life Science Alliance
● 285 papers in training set
Top 9%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.