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 \"CanvasXpress R Library\"\noutput: \n    html_document:\n        self_contained: no\n---\n\n\u003ca href=\"https://www.canvasxpress.org\"\u003e\u003cimg src=\"vignettes/images/hexagon.png\" align=\"left\" width=\"175\"\u003e\u003c/a\u003e\n\n\u003c!-- Badge Location --\u003e\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/canvasXpress?color=9bc2cf)](https://cran.r-project.org/package=canvasXpress)\n[![CRAN_Downloads_Badge](https://cranlogs.r-pkg.org/badges/grand-total/canvasXpress?color=9bc2cf)](https://cran.r-project.org/package=canvasXpress)\n[![CDNJ version](https://img.shields.io/cdnjs/v/canvasXpress.svg)](https://cdnjs.com/libraries/canvasXpress)\n[![Coverage Status](https://img.shields.io/codecov/c/gh/cb4ds/canvasXpress/master.svg)](https://app.codecov.io/gh/cb4ds/canvasXpress?branch=master)\n\u003c!-- End Badges --\u003e\n\n***canvasXpress*** was developed as the core visualization component for bioinformatics and systems biology analysis.\nIt supports a large number of [visualizations ](https://www.canvasxpress.org/examples.html) to display scientific and non-scientific\ndata. ***canvasXpress*** also includes a simple and unobtrusive [user interface](https://www.canvasxpress.org/docs/interface.html) to explore complex data sets, a sophisticated and unique mechanism to keep track of all user customization for [Reproducible Research ](https://www.canvasxpress.org/docs/audit.html) purposes, as well as an 'out of the box'\nbroadcasting capability to synchronize selected data points in all ***canvasXpress*** plots in a page. Data can\nbe easily sorted, grouped, transposed, transformed or clustered dynamically. The fully customizable mouse events\nas well as the zooming, panning and drag-and-drop capabilities are features that make this library unique in its\nclass.\n\n***canvasXpress*** can be now simply used within R at the console to generate conventional plots, in R-Studio\nor seamlessly embedded in [Shiny](https://shiny.posit.co) web applications. Full-fledged examples of the ***canvasXpress*** library including the mouse events, zooming, and broadcasting capabilities are included in this package in several examples that can be accessed using the cxShinyExample function.  This ***canvasXpress*** R library was created with the [htmlwidgets](https://github.com/ramnathv/htmlwidgets) package.\n\n### Installation\n\ncanvasXpress is available for installation from \n[CRAN](https://CRAN.R-project.org/package=canvasXpress) or you can install the\nlatest version of ***canvasXpress*** from GitHub as follows:\n\n```r\ndevtools::install_github('neuhausi/canvasXpress')\n```\n\n### Examples\n\nThese are included to get you started on basic charting - there are many more\nexamples (including complex and compound visualizations) with R code available \nin the Examples section of the main website at \n[https://www.canvasxpress.org](https://www.canvasxpress.org)\n\n#### Scatter 3D Plot\n\n```r\ny \u003c- read.table(\"https://www.canvasxpress.org/data/cX-irist-dat.txt\", header=TRUE, sep=\"\\t\", \n                quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\nz \u003c- read.table(\"https://www.canvasxpress.org/data/cX-irist-var.txt\", header=TRUE, sep= \"\\t\", \n                quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\n\ncanvasXpress(data      = y,\n             varAnnot  = z,\n             graphType =\"Scatter3D\",\n             colorBy   = \"Species\",\n             ellipseBy = \"Species\",\n             xAxis     = list(\"Sepal.Length\"),\n             yAxis     = list(\"Petal.Width\"),\n             zAxis     = list(\"Petal.Length\"),\n             theme     = \"CanvasXpress\",\n             title     = \"Iris Data Set\",\n             axisTickScaleFontFactor  = 0.5,\n             axisTitleScaleFontFactor = 0.5)\n```\n![Scatter3D](vignettes/images/R-Scatter3D.png)\n\n#### Scatter 2D Matrix Plot\n\n```r\ny \u003c- read.table(\"https://www.canvasxpress.org/data/cX-irist-dat.txt\", header=TRUE, sep=\"\\t\", \n                quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\nz \u003c- read.table(\"https://www.canvasxpress.org/data/cX-irist-var.txt\", header=TRUE, sep= \"\\t\", \n                quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\n\ncanvasXpress(data              = y,\n             varAnnot          = z,\n             graphType         = \"Scatter2D\",\n             colorBy           = \"Species\",\n             layoutAdjust      = TRUE,\n             scatterPlotMatrix = TRUE,\n             theme             = \"CanvasXpress\")\n```\n![Scatter2DMatrix](vignettes/images/R-Scatter2DMatrix.png)\n\n#### Boxplot\n\n```r\ny \u003c- read.table(\"https://www.canvasxpress.org/data/cX-toothgrowth-dat.txt\", header=TRUE, sep=\"\\t\", \n                quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\nx \u003c- read.table(\"https://www.canvasxpress.org/data/cX-toothgrowth-smp.txt\", header=TRUE, sep=\"\\t\", \n                quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\n\ncanvasXpress(data                  = y,\n             smpAnnot              = x,\n             graphType             = \"Boxplot\",\n             groupingFactors       = list(\"dose\", \"supp\"),\n             stringSampleFactors   = list(\"dose\"),\n             graphOrientation      = \"vertical\",\n             colorBy               = \"dose\",\n             title                 = \"The Effect of Vitamin C on Tooth Growth in Guinea Pigs\",\n             smpTitle              = \"dose\",\n             xAxisTitle            = \"len\",\n             smpLabelRotate        = 90,\n             xAxisMinorTicks       = FALSE,\n             xAxis2Show            = FALSE,\n             legendScaleFontFactor = 1.8)\n```\n![Boxplot](vignettes/images/R-Boxplot.png)\n\n#### Heatmap (Multi-dimensional)\n\n```r\ny  \u003c- read.table(\"https://www.canvasxpress.org/data/cX-multidimensionalheatmap-dat.txt\", header=TRUE, sep=\"\\t\", \n                 quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\ny2 \u003c- read.table(\"https://www.canvasxpress.org/data/cX-multidimensionalheatmap-dat2.txt\", header=TRUE, sep=\"\\t\", \n                 quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\ny3 \u003c- read.table(\"https://www.canvasxpress.org/data/cX-multidimensionalheatmap-dat3.txt\", header=TRUE, sep=\"\\t\", \n                 quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\ny4 \u003c- read.table(\"https://www.canvasxpress.org/data/cX-multidimensionalheatmap-dat4.txt\", header=TRUE, sep=\"\\t\", \n                 quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\nx  \u003c- read.table(\"https://www.canvasxpress.org/data/cX-multidimensionalheatmap-smp.txt\", header=TRUE, sep= \"\\t\", \n                 quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\nz  \u003c- read.table(\"https://www.canvasxpress.org/data/cX-multidimensionalheatmap-var.txt\", header=TRUE, sep= \"\\t\", \n                 quote=\"\", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)\n\ncanvasXpress(data                 = list(y = y, data2 = y2, data3 = y3, data4 = y4),\n             smpAnnot             = x,\n             varAnnot             = z,\n             graphType            = \"Heatmap\",\n             guides               = TRUE,\n             outlineBy            = \"Outline\",\n             outlineByData        = \"data2\",\n             shapeBy              = \"Shape\",\n             shapeByData          = \"data3\",\n             sizeBy               = \"Size\",\n             sizeByData           = \"data4\",\n             showHeatmapIndicator = FALSE,\n             afterRender          = list(list(\"clusterSamples\")))\n```\n![Heatmap](vignettes/images/R-Heatmap.png)\n\n#### Four way Venn Diagram\n\n```r\ncanvasXpress(vennData   = data.frame(AC=456, A=340, ABC=552, ABCD=148, BC=915, ACD=298, BCD=613, \n                                     B=562, CD=143, ABD=578, C=620, D=592, AB=639, BD=354, AD=257),\n             graphType  = \"Venn\",\n             vennLegend = list(A=\"List 1\", D=\"List 4\", C=\"List 3\", B=\"List 2\"),\n             vennGroups = 4)\n```\n![Venn](vignettes/images/R-Venn.png)\n\n\n### More Examples and Resources\n\nIn addition to the built-in package documentation there are vignettes with \nmore information on getting started and additional examples:\n\n```r\n#List all package vignettes\nvignette(package = \"canvasXpress\")\n\n#View a specific vignette\nvignette(\"getting_started\", package = \"canvasXpress\")\nvignette(\"additional_examples\", package = \"canvasXpress\")\n```\n\nFor the use of canvasXpress plots in shiny there are interactive examples available through the\npackage function *cxShinyExample*\n\n```r\n#List example names\ncxShinyExample()\n\n#Run an interactive shiny example\ncxShinyExample(example = \"example1\")\n```\n\nThere is also a wealth of additional information including full API documentation \nand extensive R and JavaScript examples at [https://www.canvasxpress.org](https://www.canvasxpress.org).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneuhausi%2FcanvasXpress","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneuhausi%2FcanvasXpress","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneuhausi%2FcanvasXpress/lists"}