ggplot2

Wickham, Hadley

doi:10.1002/wics.147

Cited by 2,844 publications

(1,752 citation statements)

References 6 publications

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“…The relative density of cyclist crashes is clearly higher in urban centres, however, and is clearly absent from the motorway network. The extent to which bicycle crashes are concentrated in urban areas, and especially Leeds, becomes clear when Kernel Density Estimate (KDE) levels are used to avoid the information loss associated with 'overplotting' (Wickham, 2011). This is presented in Fig.…”

Section: Where Are Crashes Most Likely To Happen?mentioning

confidence: 99%

Who, where, when: the demographic and geographic distribution of bicycle crashes in West Yorkshire

Lovelace

Roberts

Kellar

2016

Transportation Research Part F: Traffic Psychology and Behaviou

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Factors associated with cycle safety, including international differences in injury and mortality rates, protective equipment and bicycle training, have been subject to increasing academic interest. Environmental variables associated with cycle safety have also been scrutinised, but few studies have focussed on geographical factors at the local level. This paper addresses this research gap by analysing a geo-referenced dataset of road traffic incidents, taken from the UK's STATS19 dataset (2005 -2012). We investigate incidents involving cyclists within West Yorkshire. This is an interesting case study area as it has an historically low cycling rate but very ambitions cycling plans following investment from the Department of Transport. West Yorkshire is found to be an unusually risky area for cyclists, with an estimated 53 deaths and 1372 serious injuries per billion kilometres cycled, based on census commuting statistics. This is roughly double the national average. This riskiness varies spatially and temporally, broadly in line with expectations from the previous literature. An unexpected result was that cycling seems to be disproportionately risky for young people in West Yorkshire compared with young people nationally. The case study raises the issue of potential negative health impacts of promoting cycling amongst vulnerable groups in dangerous areas. We conclude by highlighting opportunities for increasing cycling uptake via measures designed primarily to improve safety. The analysis underlying this research is reproducible, based on code stored at github.com/Robinlovelace/bikeR.

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Section: Where Are Crashes Most Likely To Happen?mentioning

confidence: 99%

Who, where, when: the demographic and geographic distribution of bicycle crashes in West Yorkshire

Lovelace

Roberts

Kellar

2016

Transportation Research Part F: Traffic Psychology and Behaviou

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“…To visualize these results we performed regularized log transformation to the original occurrence tables for all 20 clusters using DESeq2 [84]. The results were plotted using ggplot2 [85].…”

Section: Orthology and Molecular Species Phylogenymentioning

confidence: 99%

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

et al. 2014

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Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range. Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism. Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

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“…Measurements of differential abundance were statistically significant if the adjusted p-value was < 0.05 (-log10 adjusted p-value = 1.3). The graphics were performed in the ggplot package [42]. …”

Section: Methodsmentioning

confidence: 99%

In situ substrate-formed biofilms using IDODS mimic supragingival tooth-formed biofilms

Tomás

Prada-López

Quintas

et al. 2018

Journal of Oral Microbiology

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This study aimed to compare the bacterial viability and diversity of a substrate-formed biofilm (SF-biofilm) in situ to a supragingival tooth-formed biofilm (TF-biofilm) in the same group of individuals. The impact of the device/disc position and toothbrushing during the formation of SF-biofilm was also assessed. Two tests were run. In test 1, 15 volunteers wore two hemi-splints carrying six discs of human enamel, glass, and hydroxyapatite for 2 days, and were instructed to not perform any oral hygiene measure. Biofilm samples were collected from the substrates and the contralateral tooth and were analysed using CLSM. In five volunteers, half of the biofilm present on the discs and their contralateral teeth were scraped and analysed using 16S pyrosequencing. In test 2, the microscopic analysis was repeated only on the SF-biofilm samples, and the volunteers were allowed to brush their teeth. Multivariate analyses revealed that the donors had a significant effect on the composition of the biofilm, confirming its subject-dependent character. The bacterial composition of the SF-biofilm was similar to the TF-biofilm, with significant differential abundance detected in very few taxa of low abundance. The toothbrushing during the formation of SF-biofilm was the only factor that conditioned the thickness or bacterial viability.

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ggplot2

Cited by 2,844 publications

References 6 publications

Who, where, when: the demographic and geographic distribution of bicycle crashes in West Yorkshire

Who, where, when: the demographic and geographic distribution of bicycle crashes in West Yorkshire

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

In situ substrate-formed biofilms using IDODS mimic supragingival tooth-formed biofilms

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