TCGA Expression Data Density Plot
The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that has generated a vast amount of multi-omics data, including genomic, epigenomic, and transcriptomic information. This data is invaluable for researchers seeking to understand the complexities of cancer and develop novel diagnostic and therapeutic strategies. TCGA data can be visualized and analyzed through various graph-based approaches, offering powerful ways to explore relationships and patterns within the data. Graph representations of TCGA data are particularly useful in visualizing complex networks of interactions between genes, proteins, and other biological molecules. These graphs can be used to identify key driver mutations, discover novel therapeutic targets, and predict patient prognosis. Such analyses require specialized bioinformatics tools and expertise to manage and interpret the large and complex datasets generated by TCGA. The insights gleaned from TCGA graphs are contributing significantly to cancer research and personalized medicine. Data obtained from Facilitating Exploratory Data Visualization: Application to TCGA Genomic Data.
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}
}
// Create the configuration for the graph
var config = {
"colorBy" : "dataset",
"colorScheme" : "JCO",
"graphType" : "Scatter2D",
"hideHistogram" : false,
"histogramBins" : 15,
"histogramType" : "staggered",
"layoutTopology" : "1X3",
"legendColumns" : 3,
"legendKeyBackgroundBorderColor" : "rgba(255,255,255,0)",
"legendKeyBackgroundColor" : "rgba(255,255,255,0)",
"legendPosition" : "top",
"legendTextScaleFontFactor" : 1.5,
"segregateVariablesBy" : ["dataset"],
"showFilledHistogramDensity" : true,
"showHistogram" : "dataset",
"showHistogramBars" : true,
"showHistogramDensity" : true,
"showHistogramMedian" : false,
"stripBackgroundBorderColor" : "rgb(0,0,0)",
"stripBackgroundColor" : "rgba(0,0,0,0)",
"stripTextColor" : "rgb(0,0,0)",
"toolbarType" : "over",
"xAxisRugShow" : false,
"xAxisTitle" : "Expression",
"yAxisTitle" : "Density",
"xAxis": ["GATA3","PTEN","XBP1"]
}
// 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-exprtcgat-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-exprtcgat-var.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
data=y,
varAnnot=z,
colorBy="dataset",
colorScheme="JCO",
graphType="Scatter2D",
hideHistogram=FALSE,
histogramBins=15,
histogramType="staggered",
layoutTopology="1X3",
legendColumns=3,
legendKeyBackgroundBorderColor="rgba(255,255,255,0)",
legendKeyBackgroundColor="rgba(255,255,255,0)",
legendPosition="top",
legendTextScaleFontFactor=1.5,
segregateVariablesBy=list("dataset"),
showFilledHistogramDensity=TRUE,
showHistogram="dataset",
showHistogramBars=TRUE,
showHistogramDensity=TRUE,
showHistogramMedian=FALSE,
stripBackgroundBorderColor="rgb(0,0,0)",
stripBackgroundColor="rgba(0,0,0,0)",
stripTextColor="rgb(0,0,0)",
toolbarType="over",
xAxis=list("GATA3", "PTEN", "XBP1"),
xAxisRugShow=FALSE,
xAxisTitle="Expression",
yAxisTitle="Density"
)
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 = "tcga7",
data = {
"y": {
"data": [
[2.87, 1.36, 2.98],
[2.17, 0.43, 2.55],
[1.32, 1.31, 3.02],
[1.84, 0.81, 3.13],
[-6.03, 0.25, -1.45],
[1.8, 1.31, 4.04],
[-4.88, -0.24, -0.72],
[-3.14, -1.24, -1.19],
[2.03, 1.21, 2.28],
[-0.29, 0.29, -1.6],
[-0.8, -0.17, 0.33],
[2.65, 0.58, 3.06],
[-2.31, 0, -1.18],
[-3.76, 0.46, -2.44],
[3.93, 0.71, 2.09],
[-1.28, 0.37, 1.72],
[1.62, 0.92, 2.01],
[1.87, -0.04, 1.18],
[1.47, 0.15, 1.51],
[-2.96, 1.36, -1.15],
[2.35, 0.94, 0.96],
[2.46, 0.64, 2.45],
[3.37, -0.14, 2.45],
[2.98, 0.27, 3.19],
[2.26, 0.47, 2.78],
[1.99, 0.98, 1.44],
[1.54, 0.46, 1.62],
[1.48, 0.86, 1.03],
[0.04, 0.64, 1.14],
[2.31, 0.98, 0.42],
[-2.2, 0.34, -1.81],
[1.82, 1.1, 2.16],
[-1.29, -0.7, -0.87],
[2.98, 0.27, 2.93],
[2.13, -0.13, 2.48],
[1.99, 1.36, 2.36],
[1.38, 0.78, 1.93],
[1.8, 1.25, 2.48],
[1.83, 0.73, 1.88],
[2.95, 1.03, 3.49],
[0.79, 1.12, 3.35],
[2.79, 1.01, 1.88],
[2.64, 0.55, 3.47],
[1.71, 0.93, 2.53],
[1.55, 1.34, 2.54],
[1.76, 1.09, 2.3],
[1.22, 0.4, 2.71],
[-0.08, 1.11, 0.6],
[2.83, 0.56, 2.29],
[1.83, 0.34, 1.88],
[0.36, 0.82, 1.5],
[-1.74, 1.22, 0.38],
[2.09, 1.25, 3.7],
[0.34, -0.55, 0.84],
[0.11, 0.39, 1.44],
[0.16, -1.12, -1.75],
[2.12, 1.27, 2.98],
[2.37, 1.14, 2.48],
[1.94, 0.94, 2.68],
[1.93, 1.39, 1.27],
[1.7, 1.09, 1.91],
[2.25, 2.2, 4.03],
[2.19, 0.86, 2.15],
[-2.94, -1.58, -0.92],
[1.73, 0.85, 2.74],
[1.43, 0.28, 2.14],
[2.02, 0.9, 3.27],
[2.33, 0.2, 3.73],
[-4.57, 0.66, -1.4],
[1.43, 1.19, 2.21],
[1.97, 1.56, 2.26],
[-2.71, 0.46, -1.59],
[1.5, 0.42, 2.03],
[3.14, 0.62, 3.44],
[0, 1.69, 3.2],
[-1.03, 0.05, -1.26],
[1.22, 1.57, 1.05],
[0.32, 0.88, 1.36],
[2.48, 0.62, 3.02],
[2.42, 0.02, 2.3],
[-3.25, 2.04, -1.67],
[2.84, 0.92, 3.13],
[-1.06, 0.48, -0.78],
[-3.86, 1.7, -1.38],
[1.93, -0.42, 2.06],
[-1.75, -0.43, -1.21],
[-0.43, 1.75, 0.85],
[-4.4, 0.83, -1.34],
[-0.75, 1.92, -0.07],
[2.26, 1.07, 3.16],
[3.32, -0.1, 3.65],
[0.79, -0.26, 3.21],
[1.6, 0.84, 1.85],
[0.89, -0.04, 3.24],
[1.1, 0.53, 1.28],
[2.38, 1.04, 2.52],
[2.67, 0, 2.71],
[3.71, 0.65, 0.9],
[2.98, 0.52, 1.29],
[1.44, 0.73, 2.89],
[1.71, 0.59, 2.24],
[1.62, 0.67, 1.96],
[2.6, 0.44, 2.93],
[2.12, 0.89, 2.01],
[-4.39, -0.18, -1.12],
[1.21, 0.77, 2.23],
[1.93, 1.09, 2.88],
[1.74, 0.88, 3.05],
[1.54, 1.23, 4.3],
[2.47, 0.96, 1.48],
[2.15, 0.67, 3.34],
[-2.05, 0.73, -1],
[1.14, 0.76, 3.73],
[-0.93, -0.1, -0.52],
[2.73, 1.31, 3.77],
[-0.69, 0.55, 1.16],
[0.89, 0.83, 2.3],
[3.15, 0.82, 3.08],
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[2.34, 0.48, 2.77],
[3.87, 0.5, 3.52],
[2.33, 0.41, 2.5],
[2.07, 1.18, 2.29],
[1.82, 0.89, 2.34],
[2.42, -0.73, 2.67],
[2.15, 0.29, 2.84],
[2.65, 0.73, 2.38],
[1.51, 0.08, 2.38],
[3.34, 0.56, 3.45],
[-1.37, 0.73, -0.71],
[1.4, 0.63, 2.51],
[2.34, 0.87, 0.35],
[0.88, 0.56, 2.05],
[2.41, 1.05, 2.62],
[0.92, 0.56, 2.29],
[-3.77, 0.42, 0.53],
[2.63, 1.1, 3.12],
[2.28, 0.52, 2.5],
[-1.91, 0.57, 1.61],
[2.44, 0.94, 1.7],
[2.42, 0.86, 1.73],
[3.51, 0.61, 3.82],
[1.58, 0.79, 3.12],
[2.27, 0.46, 2.97],
[-0.4, 0.35, 2.69],
[2.12, 1.18, 3.02],
[1.46, 1.66, 3.33],
[1.27, 0.55, 1.79],
[2.35, 1.13, 4.49],
[2.36, 0.71, 3.17],
[2.38, 0.52, 3.37],
[2.13, 0.68, 1.95],
[2.24, 1.07, 2.83],
[2.27, -0.21, 3.45],
[0.34, 1.4, 3.06],
[2.35, 0.77, 2.46],
[3.49, -0.11, 3.82],
[0.92, -1.34, 3.29],
[2.12, 1.29, 3.13],
[1.64, 0.68, 2.48],
[1.98, 1.14, 2.36],
[2.04, -0.5, 2.32],
[2.52, 0.57, 3.42],
[1.12, 0.48, 1.48],
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[2.45, -0.37, 1.89],
[2.7, 0.89, 3.35],
[2.84, -0.77, 4.03],
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[3, -0.07, 3.42],
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[1.87, 1.17, 2.81],
[-0.16, 0.61, 1.27],
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[1.62, 0.49, 2.28],
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[-1.71, 1.14, 0.73],
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[2.57, 0.3, 3.94],
[2.28, 0.69, 2.09],
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[-2.24, 0.26, -0.23],
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"LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC", "LUSC"]
}
},
config = {
"colorBy": "dataset",
"colorScheme": "JCO",
"graphType": "Scatter2D",
"hideHistogram": False,
"histogramBins": 15,
"histogramType": "staggered",
"layoutTopology": "1X3",
"legendColumns": 3,
"legendKeyBackgroundBorderColor": "rgba(255,255,255,0)",
"legendKeyBackgroundColor": "rgba(255,255,255,0)",
"legendPosition": "top",
"legendTextScaleFontFactor": 1.5,
"segregateVariablesBy": ["dataset"],
"showFilledHistogramDensity": True,
"showHistogram": "dataset",
"showHistogramBars": True,
"showHistogramDensity": True,
"showHistogramMedian": False,
"stripBackgroundBorderColor": "rgb(0,0,0)",
"stripBackgroundColor": "rgba(0,0,0,0)",
"stripTextColor": "rgb(0,0,0)",
"toolbarType": "over",
"xAxisRugShow": False,
"xAxisTitle": "Expression",
"yAxisTitle": "Density",
"xAxis": ["GATA3", "PTEN", "XBP1"]
},
width = 600,
height = 550
)
# 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 = "tcga7",
data = {
"y": {
"data": [
[2.87, 1.36, 2.98],
[2.17, 0.43, 2.55],
[1.32, 1.31, 3.02],
[1.84, 0.81, 3.13],
[-6.03, 0.25, -1.45],
[1.8, 1.31, 4.04],
[-4.88, -0.24, -0.72],
[-3.14, -1.24, -1.19],
[2.03, 1.21, 2.28],
[-0.29, 0.29, -1.6],
[-0.8, -0.17, 0.33],
[2.65, 0.58, 3.06],
[-2.31, 0, -1.18],
[-3.76, 0.46, -2.44],
[3.93, 0.71, 2.09],
[-1.28, 0.37, 1.72],
[1.62, 0.92, 2.01],
[1.87, -0.04, 1.18],
[1.47, 0.15, 1.51],
[-2.96, 1.36, -1.15],
[2.35, 0.94, 0.96],
[2.46, 0.64, 2.45],
[3.37, -0.14, 2.45],
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[1.48, 0.86, 1.03],
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[0.32, 0.88, 1.36],
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[-2.05, 0.73, -1],
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},
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}
},
config = {
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"colorScheme": "JCO",
"graphType": "Scatter2D",
"hideHistogram": False,
"histogramBins": 15,
"histogramType": "staggered",
"layoutTopology": "1X3",
"legendColumns": 3,
"legendKeyBackgroundBorderColor": "rgba(255,255,255,0)",
"legendKeyBackgroundColor": "rgba(255,255,255,0)",
"legendPosition": "top",
"legendTextScaleFontFactor": 1.5,
"segregateVariablesBy": ["dataset"],
"showFilledHistogramDensity": True,
"showHistogram": "dataset",
"showHistogramBars": True,
"showHistogramDensity": True,
"showHistogramMedian": False,
"stripBackgroundBorderColor": "rgb(0,0,0)",
"stripBackgroundColor": "rgba(0,0,0,0)",
"stripTextColor": "rgb(0,0,0)",
"toolbarType": "over",
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"xAxisTitle": "Expression",
"yAxisTitle": "Density",
"xAxis": ["GATA3", "PTEN", "XBP1"]
},
width = 600,
height = 550
)
)
