raincloud plots  (Tajima Shoji Co Ltd)

Journal: Heredity

Article Title: Genome sequence analysis provides evidence that a boreal crustacean colonised Svalbard well before the ongoing Atlantification of the Arctic

doi: 10.1038/s41437-025-00793-7

Figure Lengend Snippet: Raincloud plots of the genome-wide distribution of nucleotide diversity ( A ) and Tajima’s D ( B ) values within the four populations identified by the structure analyses.

Article Snippet: Raincloud plots in R illustrated the distribution of nucleotide diversity and Tajima’s D (Tajima ) values along the genome.

Techniques: Genome Wide

Journal: NAR Genomics and Bioinformatics

Article Title: Distribution of specific prokaryotic immune systems correlates with host optimal growth temperature

doi: 10.1093/nargab/lqae105

Figure Lengend Snippet: Distribution of immune systems in different phyla and in correlation to genome size. ( A ) Percentage of SR-GTDB genomes that encodes a specific immune system family, subdivided for the prokaryotic phyla. Only immune system families identified in ≥ 150 genomes are shown; genomes from phyla with < 30 accessions in the SR-GTDB are grouped as ‘other bacteria’ or ‘other archaea’. ( B ) Distribution of the total number of immune systems encoded in prokaryotes in the SR-GTDB for different phyla, represented by raincloud plots (visualizing individual data points as well as the probability density of the data) and a boxplot. The median is indicated in the boxplot, while the average (Av) is shown on the right. ( C ) Distribution of genome sizes for prokaryotes in the SR-GTDB for different phyla, represented by a raincloud plot and a boxplot, with averages indicated. ( D ) Correlation between (i) number of immune systems encoded and (ii) genome size for both bacteria (blue) and archaea (orange) represented in the SR-GTDB. Pearson correlation coefficients ( r ) and P -values are indicated. ( E ) Percentage of genomes encoding specific immune system families for different genome size categories. Only immune system families identified in ≥ 150 genomes are shown.

Article Snippet: Bar graphs, scatter plots, pie charts and heat maps were made using Microsoft Excel and Adobe Illustrator, with the exception of the Sankey diagram [made using SankeyMATIC ( https://sankeymatic.com/ )], raincloud and bee-swarm plots (made using python package Plotly version 5.14.0) and the Venn diagram (made using the function venn2 of the python package matplotlib-venn version 0.11.7).

Techniques: Bacteria

Journal: NAR Genomics and Bioinformatics

Article Title: Distribution of specific prokaryotic immune systems correlates with host optimal growth temperature

doi: 10.1093/nargab/lqae105

Figure Lengend Snippet: Distribution of immune systems in different T opt categories. ( A ) Definition of T opt categories and their bacterial and archaeal coverage in the SR-GTDB. ( B ) Distribution of genomes in the SR-GTDB for different T opt categories and phyla, with averages indicated. Genomes from phyla with < 30 accessions are grouped as ‘other bacteria’ and ‘other archaea’. ( C ) Distribution of the total number of immune systems in bacteria in the SR-GTDB per T opt category, represented by a raincloud plot (visualizing both individual data points and the probability density of the data) and a boxplot. The median is indicated in the boxplot, while the average (Av) is shown on the right. ( D ) Distribution of bacterial genome sizes for different T opt categories, represented by raincloud plots (visualizing both individual data points and the probability density of the data) and a boxplot. The median is indicated in the boxplot, while the average (Av) is shown on the right. ( E ) Percentage of bacterial genomes encoding specific immune system families (when found in ≥ 150 genomes) for different T opt categories. *, ** and *** indicate P -values < 1.43 × 10 −3 , 1.43 × 10 −4 and 1.43 × 10 −5 . P -values are determined by a χ 2 test of independence; cut-off values are determined by a Bonferroni test of α = 0.05 / number of comparisons. ( F ) Proportional distribution of different immune system categories for different T opt categories in bacteria. ( G ) Percentage of bacterial genomes with specific RM, CRISPR-Cas and pAgo subtypes identified (when found in ≥ 150 genomes) for different T opt categories. For RM, *, ** and *** indicate P -values 1.43 × 10 −3 , 1.43 × 10 −4 and 1.43 × 10 −5 . For CRISPR-Cas, *, ** and *** indicate P -values < 3.85 × 10 −3 , 3.85 × 10 −4 and 3.85 ×10 −5 . For pAgos, *, ** and *** indicate P -values < 1 × 10 −2 , 1 × 10 −3 and 1 × 10 −4 . P -values are determined by a χ 2 test of independence; cut-off values are determined by a Bonferroni test of α = 0.05 / number of comparisons.

Article Snippet: Bar graphs, scatter plots, pie charts and heat maps were made using Microsoft Excel and Adobe Illustrator, with the exception of the Sankey diagram [made using SankeyMATIC ( https://sankeymatic.com/ )], raincloud and bee-swarm plots (made using python package Plotly version 5.14.0) and the Venn diagram (made using the function venn2 of the python package matplotlib-venn version 0.11.7).

Techniques: Bacteria, CRISPR

Journal: Cerebellum (London, England)

Article Title: The Effect of Nucleo-Olivary Stimulation on Climbing Fiber EPSPs in Purkinje Cells

doi: 10.1007/s12311-024-01682-1

Figure Lengend Snippet: Effect of nucleo-olivary stimulation on CFR EPSP distribution. A. Comparison of EPSP counts in peri-orbitally elicited climbing fiber responses with or without preceding nucleo-olivary stimulation. B. Same as A, but with all trials in which the periorbital stimulation did not elicit a response were excluded. Both figures display probability density function (PDF), and boxplots using raincloud plots package for Matlab (see for details)

Article Snippet: Both figures display probability density function (PDF), and boxplots using raincloud plots package for Matlab (see [ ] for details)

Techniques: Comparison