2D Data Relationships with Line Object
Scatter2D graphs are a fundamental visualization tool used to display the relationship between two numerical variables. Each data point is represented as a dot on a two-dimensional plane, where the x-coordinate and y-coordinate correspond to the values of the two variables. This allows for quick identification of trends, clusters, and outliers in the data. Applications range from scientific data analysis to business intelligence, making them highly versatile. Creating effective Scatter2D graphs involves careful consideration of axis scaling, labeling, and color-coding. Highlighting specific data points or regions can improve understanding. Interactive Scatter2D plots further enhance exploration, allowing users to zoom, pan, and select individual data points for detailed examination. Choosing appropriate visualization tools greatly impacts the ability to draw meaningful insights from data.
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// Use a data frame (2D-array) for the graph
var data = [
[ "Id", "AveExpr", "logFC", "-log-pVal", "Group", "FC"],
[ "Gene1", 0.94, 1.399, 3.5508, "Increased", "3.0"],
[ "Gene2", 0.923, 1.917, 3.3186, "Increased", "3.0"],
[ "Gene3", -0.234, -1.15, 2.8226, "Decreased", "2.0"],
[ "Gene4", 0.326, -1.329, 2.7428, "Decreased", "2.0"],
[ "Gene5", 0.159, -1.05, 2.5841, "Decreased", "2.0"],
[ "Gene6", 0.062, -0.896, 2.4041, "Decreased", "2.0"],
[ "Gene7", -0.057, 1.006, 2.1794, "Increased", "2.0"],
[ "Gene8", 0.004, -1.016, 2.0992, "Decreased", "2.0"],
[ "Gene9", -0.23, 0.816, 2.0522, "Increased", "2.0"],
[ "Gene10", -0.134, 1.174, 2.0317, "Increased", "2.0"],
[ "Gene11", 0.024, -0.648, 2.003, "Decreased", "2.0"],
[ "Gene12", 0.298, -0.621, 1.999, "Decreased", "1.0"],
[ "Gene13", -0.246, -0.576, 1.8406, "Decreased", "1.0"],
[ "Gene14", -0.416, 1.327, 1.8405, "Increased", "1.0"],
[ "Gene15", -0.149, 0.74, 1.8137, "Increased", "1.0"],
[ "Gene16", 0.144, 0.624, 1.7512, "Increased", "1.0"],
[ "Gene17", -0.134, 0.626, 1.7371, "Increased", "1.0"],
[ "Gene18", -0.25, -0.873, 1.716, "Decreased", "1.0"],
[ "Gene19", 0.109, -0.944, 1.655, "Decreased", "1.0"],
[ "Gene20", 0.155, -0.671, 1.6509, "Decreased", "1.0"],
[ "Gene21", 0.022, 0.616, 1.633, "Increased", "1.0"],
[ "Gene22", -0.154, -0.519, 1.5754, "Decreased", "1.0"],
[ "Gene23", 0.133, 0.912, 1.5739, "Increased", "1.0"],
[ "Gene24", 0.032, 0.692, 1.5642, "Increased", "1.0"],
[ "Gene25", 0.215, -0.601, 1.5373, "Decreased", "1.0"],
[ "Gene26", -0.052, 0.576, 1.5266, "Increased", "1.0"],
[ "Gene27", 0.233, 0.534, 1.5025, "Increased", "1.0"],
[ "Gene28", 0.103, -0.531, 1.4939, "Decreased", "1.0"],
// ... (data truncated after 29 records for clarity)
]
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"backgroundType": "panel",
"colorBy": "Group",
"colors": ["rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"],
"decorations": {
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"width": 2,
"y": 0.5
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"color": "rgba(0,104,139,0.5)",
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"y": -0.5
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"showDecorations": true,
"showLoessFit": true,
"showTransition": false,
"sizeBy": "FC",
"sizes": [4, 12, 14, 15, 16, 17, 18],
"title": "Profile plot",
"xAxis": ["AveExpr"],
"xAxisGridMajorColor": "rgb(255,255,255)",
"yAxis": ["logFC"],
"yAxisGridMajorColor": "rgb(255,255,255)"
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}
}
// Create the configuration for the graph
var config = {
"axisAlgorithm": "rPretty",
"backgroundType": "panel",
"colorBy": "Group",
"colors": ["rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"],
"decorations": {
"line": [
{
"color": "rgba(205,0,0,0.5)",
"width": 2,
"y": 0.5
},
{
"color": "rgba(0,104,139,0.5)",
"width": 2,
"y": -0.5
}
]
},
"graphType": "Scatter2D",
"legendBackgroundColor": "rgb(238,238,238)",
"legendBox": true,
"legendBoxColor": "rgb(0,0,0)",
"legendInside": true,
"legendPosition": "bottomRight",
"panelBackgroundColor": "rgb(238,238,238)",
"showConfidenceIntervals": false,
"showDecorations": true,
"showLoessFit": true,
"showTransition": false,
"sizeBy": "FC",
"sizes": [4, 12, 14, 15, 16, 17, 18],
"title": "Profile plot",
"xAxis": ["AveExpr"],
"xAxisGridMajorColor": "rgb(255,255,255)",
"yAxis": ["logFC"],
"yAxisGridMajorColor": "rgb(255,255,255)"
}
// 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-scatterR-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
z=read.table("https://www.canvasxpress.org/data/r/cX-scatterR-var.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
data=y,
varAnnot=z,
axisAlgorithm="rPretty",
backgroundType="panel",
colorBy="Group",
colors=list("rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"),
decorations=list(line=list(list(color="rgba(205,0,0,0.5)", width=2, y=0.5), list(color="rgba(0,104,139,0.5)", width=2, y=-0.5))),
graphType="Scatter2D",
legendBackgroundColor="rgb(238,238,238)",
legendBox=TRUE,
legendBoxColor="rgb(0,0,0)",
legendInside=TRUE,
legendPosition="bottomRight",
panelBackgroundColor="rgb(238,238,238)",
showConfidenceIntervals=FALSE,
showDecorations=TRUE,
showLoessFit=TRUE,
showTransition=FALSE,
sizeBy="FC",
sizes=list(4, 12, 14, 15, 16, 17, 18),
title="Profile plot",
xAxis=list("AveExpr"),
xAxisGridMajorColor="rgb(255,255,255)",
yAxis=list("logFC"),
yAxisGridMajorColor="rgb(255,255,255)"
)
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 = "scatter2d11",
data = {
"y": {
"data": [
[0.94, 1.399, 3.5508],
[0.923, 1.917, 3.3186],
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[0.159, -1.05, 2.5841],
[0.062, -0.896, 2.4041],
[-0.057, 1.006, 2.1794],
[0.004, -1.016, 2.0992],
[-0.23, 0.816, 2.0522],
[-0.134, 1.174, 2.0317],
[0.024, -0.648, 2.003],
[0.298, -0.621, 1.999],
[-0.246, -0.576, 1.8406],
[-0.416, 1.327, 1.8405],
[-0.149, 0.74, 1.8137],
[0.144, 0.624, 1.7512],
[-0.134, 0.626, 1.7371],
[-0.25, -0.873, 1.716],
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[0.155, -0.671, 1.6509],
[0.022, 0.616, 1.633],
[-0.154, -0.519, 1.5754],
[0.133, 0.912, 1.5739],
[0.032, 0.692, 1.5642],
[0.215, -0.601, 1.5373],
[-0.052, 0.576, 1.5266],
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[-0.144, -0.562, 1.3811],
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[-0.325, -0.721, 1.2789],
[0.158, -0.477, 1.2772],
[0.026, 0.56, 1.2702],
[0.182, -0.441, 1.266],
[0.039, -0.654, 1.2501],
[0.146, -0.607, 1.2441],
[-0.101, 0.411, 1.2361],
[0.407, 0.811, 1.2338],
[-0.117, 0.76, 1.2275],
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[-0.025, 0.497, 1.0669],
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[-0.115, 0.389, 1.0542],
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[-0.218, 0.375, 0.9429],
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}
},
config = {
"axisAlgorithm": "rPretty",
"backgroundType": "panel",
"colorBy": "Group",
"colors": ["rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"],
"decorations": {
"line": [
{
"color": "rgba(205,0,0,0.5)",
"width": 2,
"y": 0.5
},
{
"color": "rgba(0,104,139,0.5)",
"width": 2,
"y": -0.5
}
]
},
"graphType": "Scatter2D",
"legendBackgroundColor": "rgb(238,238,238)",
"legendBox": True,
"legendBoxColor": "rgb(0,0,0)",
"legendInside": True,
"legendPosition": "bottomRight",
"panelBackgroundColor": "rgb(238,238,238)",
"showConfidenceIntervals": False,
"showDecorations": True,
"showLoessFit": True,
"showTransition": False,
"sizeBy": "FC",
"sizes": [4, 12, 14, 15, 16, 17, 18],
"title": "Profile plot",
"xAxis": ["AveExpr"],
"xAxisGridMajorColor": "rgb(255,255,255)",
"yAxis": ["logFC"],
"yAxisGridMajorColor": "rgb(255,255,255)"
},
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 = "scatter2d11",
data = {
"y": {
"data": [
[0.94, 1.399, 3.5508],
[0.923, 1.917, 3.3186],
[-0.234, -1.15, 2.8226],
[0.326, -1.329, 2.7428],
[0.159, -1.05, 2.5841],
[0.062, -0.896, 2.4041],
[-0.057, 1.006, 2.1794],
[0.004, -1.016, 2.0992],
[-0.23, 0.816, 2.0522],
[-0.134, 1.174, 2.0317],
[0.024, -0.648, 2.003],
[0.298, -0.621, 1.999],
[-0.246, -0.576, 1.8406],
[-0.416, 1.327, 1.8405],
[-0.149, 0.74, 1.8137],
[0.144, 0.624, 1.7512],
[-0.134, 0.626, 1.7371],
[-0.25, -0.873, 1.716],
[0.109, -0.944, 1.655],
[0.155, -0.671, 1.6509],
[0.022, 0.616, 1.633],
[-0.154, -0.519, 1.5754],
[0.133, 0.912, 1.5739],
[0.032, 0.692, 1.5642],
[0.215, -0.601, 1.5373],
[-0.052, 0.576, 1.5266],
[0.233, 0.534, 1.5025],
[0.103, -0.531, 1.4939],
[0.277, 0.545, 1.4886],
[0.654, -2.438, 1.485],
[-0.114, 0.772, 1.4845],
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[-0.002, 0.535, 1.4464],
[-0.222, 0.809, 1.4417],
[0.113, -0.544, 1.4238],
[0.15, -0.506, 1.3955],
[-0.144, -0.562, 1.3811],
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[0.165, -0.659, 1.35],
[0.096, 0.591, 1.3475],
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[-0.101, 0.411, 1.2361],
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[-0.117, 0.76, 1.2275],
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[-0.029, 0.37, 1.0126],
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[-0.37, -0.569, 0.9842],
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[-0.218, 0.375, 0.9429],
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[0.045, 0.342, 0.9312],
[0.142, 0.375, 0.9292],
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},
config = {
"axisAlgorithm": "rPretty",
"backgroundType": "panel",
"colorBy": "Group",
"colors": ["rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"],
"decorations": {
"line": [
{
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"width": 2,
"y": 0.5
},
{
"color": "rgba(0,104,139,0.5)",
"width": 2,
"y": -0.5
}
]
},
"graphType": "Scatter2D",
"legendBackgroundColor": "rgb(238,238,238)",
"legendBox": True,
"legendBoxColor": "rgb(0,0,0)",
"legendInside": True,
"legendPosition": "bottomRight",
"panelBackgroundColor": "rgb(238,238,238)",
"showConfidenceIntervals": False,
"showDecorations": True,
"showLoessFit": True,
"showTransition": False,
"sizeBy": "FC",
"sizes": [4, 12, 14, 15, 16, 17, 18],
"title": "Profile plot",
"xAxis": ["AveExpr"],
"xAxisGridMajorColor": "rgb(255,255,255)",
"yAxis": ["logFC"],
"yAxisGridMajorColor": "rgb(255,255,255)"
},
width = 600,
height = 600
)
)
