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plotly specifications


Unique identifier OMICS_16447
Name plotly
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License MIT License
Computer skills Advanced
Version 4.5.6
Stability Stable
R, ggplot2
Maintained Yes


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  • person_outline Carson Sievert <>

Additional information

plotly in publications

PMCID: 5865158
PMID: 29572470
DOI: 10.1038/s41467-018-03618-w

[…] p-value < 0.05. r with bioconductor packages; ggplots, ggthemes, colorspace were used to make plots. pca was performed with r basic function, prcomp method, and results are visualized using r plotly bioconductor package. principle components 1, 2, and 3 were used to make the three-dimensional plots. gsea was performed with xcode programming and bioconductor/r. affymetrix files […]

PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] naive bayes), randomforest (random forest), neuralnet (neural network/perceptron) and gbm (gradient boosting method). for performance assessment and visualization, we used rocr, prroc, ggplot2 and plotly packages., six popular machine-learning algorithms for binary classification were trained with default parameters. we performed 100 training/test iterations where we randomly selected 70% […]

PMCID: 5794756
PMID: 29391527
DOI: 10.1038/s41598-018-20217-3

[…] to unsupervised pc analysis using default parameters in multiexperiment viewer (mev) 4.8.1 software. data of the three pcs (pc1, pc2 and pc3) were then represented in 3d scatter plots using plotly 2.0(, differential expression analyses between sets of tumors (smarca4-high lihc versus smarca4-low lihc; smarca2-high lihc versus smarca2-low lihc; smarca4-high kirc […]

PMCID: 5749766
PMID: 29293601
DOI: 10.1371/journal.pone.0190266

[…] over 1 kbp were searched as a query with the stringent threshold (e-value < = 1e-10 and sequence identity > = 40%), and the best hits were retained. scatter plots were generated by using plotly []., the shotgun metagenome reads were filtered and assembled by using megahit [] with default k-mer options. subsequently, all contigs over 1,000 bp were used to identify the proteins […]

PMCID: 5725498
PMID: 29229905
DOI: 10.1038/s41467-017-02305-6

[…] profiles of 1422 zebrafish blood cells across all the 31,953 zebrafish genes. the implementation of the cloud service was performed using shiny (version 0.14.2),, and plotly (version 4.5.6),, r packages., statistical tests were carried out using r software packages as indicated in the figure legends and in the 'methods' section. no statistical […]

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