Paneled Boxplots with Paired Connections and Significance Annotations
Boxplot graphs, also known as box and whisker plots, offer a compelling way to visually display the distribution and summary statistics of a dataset. They present key descriptive statistics such as median, quartiles, and potential outliers, making them ideal for comparing data across different groups or identifying unusual data points. Understanding boxplot graphs is essential for data analysis. These graphs quickly reveal central tendency, spread, and skewness, providing valuable insights for decision-making. Their effectiveness in visualizing data makes them a staple in various fields, from finance and healthcare to engineering and social sciences.
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}
}
// Create the configuration for the graph
var config = {
"boxplotWhiskersType" : "single",
"colorBy" : "updown",
"colorKey" : {
"updown" : {
"up" : "rgb(224,130,20)",
"down" : "rgb(58,102,160)"
}
},
"connectBy" : "isolate",
"connectByPointColor" : true,
"connectByWidth" : 1,
"decorations" : {
"text" : [
{
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"label" : "ns",
"color" : "rgb(0,0,0)",
"panel" : 1,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
"preTransformed" : true
},
{
"value" : 3.2,
"label" : "ns",
"color" : "rgb(0,0,0)",
"panel" : 11,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
"preTransformed" : true
},
{
"value" : 3.2,
"label" : "****",
"color" : "rgb(0,0,0)",
"panel" : 2,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
"preTransformed" : true
},
{
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"label" : "ns",
"color" : "rgb(0,0,0)",
"panel" : 3,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
"preTransformed" : true
},
{
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"label" : "****",
"color" : "rgb(0,0,0)",
"panel" : 8,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
"preTransformed" : true
},
{
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"label" : "****",
"color" : "rgb(0,0,0)",
"panel" : 9,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
"preTransformed" : true
},
{
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"label" : "**",
"color" : "rgb(0,0,0)",
"panel" : 10,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
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},
{
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},
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"label" : "***",
"color" : "rgb(0,0,0)",
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},
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"panel" : 6,
"smpCenter" : true,
"labelScaleFontFactor" : 0.8,
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},
{
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}
]
},
"graphOrientation" : "vertical",
"graphType" : "Boxplot",
"groupingFactors" : [
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],
"isTransformedData" : "log10",
"layoutTopology" : "3X5",
"panelBackgroundBorderColor" : "rgb(0,0,0)",
"segregateSamplesBy" : [
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],
"showBoxplotOriginalData" : true,
"showLegend" : false,
"smpTextColor" : "rgb(0,0,0)",
"smpTextRotate" : 90,
"smpTextScaleFontFactor" : 0.7,
"smpTitle" : "Control or recent antibiotic",
"summaryType" : "iqr",
"stripBackgroundBorderColor" : "rgb(0,0,0)",
"stripTextColor" : "rgb(0,0,0)",
"stripTextFontStyle" : "bold",
"stripTextScaleFontFactor" : 0.7,
"stripBackgroundColors" : {
"APR" : "#4FB3A9",
"CID" : "#E7A6C4",
"CTO" : "#E7A6C4",
"DEL" : "#8073AC",
"ERA" : "#7FBF7B",
"GEP" : "#8073AC",
"OMA" : "#7FBF7B",
"POL" : "#E08214",
"SCH" : "#E08214",
"SPR" : "#E08214",
"SUO" : "#4C72B0",
"TRD" : "#E08214",
"ZOL" : "#8073AC"
},
"transformData" : "log10",
"xAxis" : [
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],
"xAxisGridMajorShow" : false,
"xAxisGridMinorShow" : false,
"xAxisTextColor" : "rgb(0,0,0)",
"xAxisTextScaleFontFactor" : 0.7,
"xAxisTicks" : 4,
"xAxisTicksColor" : "rgb(0,0,0)",
"xAxisTicksLength" : 0.75,
"xAxisTitle" : "Minimum inhibitory concentration (μ g ml-1)",
"xAxisTransformTicks" : true
}
// Event used to create graph (optional)
var events = false
// Call the CanvasXpress function to create the graph
var cX = new CanvasXpress("canvasId", data, config, events);
</script>
</body>
</html>
library(canvasXpress)
y=read.table("https://www.canvasxpress.org/data/r/cX-boxplot22-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
x=read.table("https://www.canvasxpress.org/data/r/cX-boxplot22-smp.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
data=y,
smpAnnot=x,
boxplotWhiskersType="single",
colorBy="updown",
colorKey=list(updown=list(down="rgb(58,102,160)", up="rgb(224,130,20)")),
connectBy="isolate",
connectByPointColor=TRUE,
connectByWidth=1,
decorations=list(text=list(list(color="rgb(0,0,0)", label="ns", labelScaleFontFactor=0.8, panel=1, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="ns", labelScaleFontFactor=0.8, panel=11, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="****", labelScaleFontFactor=0.8, panel=2, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="ns", labelScaleFontFactor=0.8, panel=3, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="****", labelScaleFontFactor=0.8, panel=8, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="****", labelScaleFontFactor=0.8, panel=9, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="**", labelScaleFontFactor=0.8, panel=10, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="****", labelScaleFontFactor=0.8, panel=12, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="****", labelScaleFontFactor=0.8, panel=5, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="***", labelScaleFontFactor=0.8, panel=7, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="*", labelScaleFontFactor=0.8, panel=4, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="ns", labelScaleFontFactor=0.8, panel=6, preTransformed="True", smpCenter="True", value=3.2), list(color="rgb(0,0,0)", label="****", labelScaleFontFactor=0.8, panel=13, preTransformed="True", smpCenter="True", value=3.2))),
graphOrientation="vertical",
graphType="Boxplot",
groupingFactors=list("xpos"),
isTransformedData="log10",
layoutTopology="3X5",
panelBackgroundBorderColor="rgb(0,0,0)",
segregateSamplesBy=list("drug"),
showBoxplotOriginalData=TRUE,
showLegend=FALSE,
smpTextColor="rgb(0,0,0)",
smpTextRotate=90,
smpTextScaleFontFactor=0.7,
smpTitle="Control or recent antibiotic",
stripBackgroundBorderColor="rgb(0,0,0)",
stripBackgroundColors=list(APR="#4FB3A9", CID="#E7A6C4", CTO="#E7A6C4", DEL="#8073AC", ERA="#7FBF7B", GEP="#8073AC", OMA="#7FBF7B", POL="#E08214", SCH="#E08214", SPR="#E08214", SUO="#4C72B0", TRD="#E08214", ZOL="#8073AC"),
stripTextColor="rgb(0,0,0)",
stripTextFontStyle="bold",
stripTextScaleFontFactor=0.7,
summaryType="iqr",
transformData="log10",
xAxis=list("mic"),
xAxisGridMajorShow=FALSE,
xAxisGridMinorShow=FALSE,
xAxisTextColor="rgb(0,0,0)",
xAxisTextScaleFontFactor=0.7,
xAxisTicks=4,
xAxisTicksColor="rgb(0,0,0)",
xAxisTicksLength=0.75,
xAxisTitle="Minimum inhibitory concentration (μ g ml-1)",
xAxisTransformTicks=TRUE
)
from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import show_in_browser
if __name__ == "__main__":
# Define the chart with its data and configuration
chart: CanvasXpress = CanvasXpress(
render_to = "boxplot22",
data = {
"y": {
"vars": ["mic"],
"smps": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", 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"xAxis": ["mic"],
"xAxisGridMajorShow": False,
"xAxisGridMinorShow": False,
"xAxisTextColor": "rgb(0,0,0)",
"xAxisTextScaleFontFactor": 0.7,
"xAxisTicks": 4,
"xAxisTicksColor": "rgb(0,0,0)",
"xAxisTicksLength": 0.75,
"xAxisTitle": "Minimum inhibitory concentration (μ g ml<sup>-1</sup>)",
"xAxisTransformTicks": True
},
width = 600,
height = 600
)
# Display the chart in its own Web page
show_in_browser(chart)
Run this notebook:
from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import graph
graph(
CanvasXpress(
render_to = "boxplot22",
data = {
"y": {
"vars": ["mic"],
"smps": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", 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"587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", 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"data": [
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"xAxisGridMinorShow": False,
"xAxisTextColor": "rgb(0,0,0)",
"xAxisTextScaleFontFactor": 0.7,
"xAxisTicks": 4,
"xAxisTicksColor": "rgb(0,0,0)",
"xAxisTicksLength": 0.75,
"xAxisTitle": "Minimum inhibitory concentration (μ g ml<sup>-1</sup>)",
"xAxisTransformTicks": True
},
width = 600,
height = 600
)
)
