Oncoprint from a Delimited Mutation Matrix
Oncoprint graphs offer a visually appealing and informative way to explore genomic alterations across multiple samples in cancer research. They condense complex data into an easily digestible format, highlighting the frequency and type of mutations, copy number variations, and other genomic events within a tumor cohort. This allows researchers to quickly identify patterns and potential therapeutic targets. These graphs typically display samples as rows and genomic alterations as columns, using color-coding to represent different mutation types or copy number changes. Oncoprints are invaluable for identifying frequently mutated genes, characterizing tumor heterogeneity, and guiding personalized cancer medicine strategies. The visualization helps researchers to understand cancer evolution and develop effective treatment plans.
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}
// Create the configuration for the graph
var config = {
"graphType": "Heatmap",
"oncoprintCNA": "data2",
"overlaysThickness": 100,
"oncoprintPresorted": true,
"oncoprintMUT": "data3"
}
// 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-oncoprint5-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
y2=read.table("https://www.canvasxpress.org/data/r/cX-oncoprint5-dat2.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
y3=read.table("https://www.canvasxpress.org/data/r/cX-oncoprint5-dat3.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
data=list(y=y, data2=y2, data3=y3),
graphType="Heatmap",
oncoprintCNA="data2",
oncoprintMUT="data3",
oncoprintPresorted=TRUE,
overlaysThickness=100
)
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 = "oncoprint5",
data = {
"y": {
"vars": ["T39", "T30", "T18", "T25", "T29", "T31", "T28", "T15", "T13", "T05", "T12", "T03", "T14", "T02", "T09", "T17", "T10", "T21", "T34", "T01", "T26", "T22", "T06", "T19", "T07", "T16", "T35", "T08", "T11", "T24", "T32", "T36", "T41", "T04", "T40", "T37", "T20", "T33", "T27", "T38", "T23"],
"smps": ["EGFR", "TP53", "MYC", "PTEN", "BRCA1", "BRCA2", "PIK3CA", "RB1", "AKT1", "KRAS", "MTOR", "ZNF140", "CCND1", "ZNF171", "ZNF096", "CDKN2A", "ZNF042", "ZNF089", "ZNF108", "ZNF051"],
"data": [
[-1.15, 2.25, 0.27, 0.28, -1.09, 0.31, -0.4, 0.55, -0.56, -0.78, 0.09, 0.71, -1.57, -0.72, -0.17, 0.84, 0.85, -0.28, -1.55, -0.62],
[2.2, 1.18, 1.28, -2.33, -0.49, 0.29, 2.09, 1.4, -0.43, 0.08, 0.18, -0.05, -0.81, -0.66, 0.59, 1.46, 0.16, -1.17, -1.29, 0.05],
[2.63, 0.99, 1.06, -1.2, -0.29, 0.55, 0.32, -0.23, 0.09, 0.4, 1.83, -0.45, -1.09, -0.23, 0.69, 1.03, -0.13, -1.13, -0.63, 0.63],
[2.61, -0.02, -0.76, -1.69, 1.72, 0.43, -1.54, -0.82, -1.04, 1.1, 0.48, -0.8, -0.94, -0.17, 1.07, 2.08, -0.35, -0.65, 0.2, 0.3],
[1.61, -0.36, -0.28, 0.55, 0.81, -0.58, -1.2, -0.43, 1.02, 1.37, 0.21, -1.46, -0.97, 0.43, 1.0, 0.33, -0.26, -0.41, 0.33, 0.17],
[1.05, -0.39, 0.5, 0.71, 0.21, -1.0, -1.14, 0.21, 1.5, 0.61, -0.63, -1.06, -0.17, 0.73, 0.56, -0.62, -0.38, 0.52, 0.71, -0.21],
[0.63, -0.64, -0.59, -0.23, -1.36, -1.14, -0.66, 0.24, 0.92, 0.21, -0.59, -0.28, 0.56, 0.04, -0.6, -0.65, 0.38, 1.25, 0.7, -1.19],
[-0.01, -0.01, 1.28, 1.01, -0.32, -1.45, -0.51, 0.59, 0.55, -0.15, -0.14, 0.06, 0.39, -0.34, -0.99, -0.29, 1.15, 0.96, -0.17, -1.27],
[-2.21, 0.64, 1.41, 1.96, -0.92, -0.73, -1.08, 0.54, 1.28, -0.82, 0.01, 0.85, 0.42, -0.77, -0.98, -0.26, 1.06, 0.84, -0.42, -0.92],
[1.08, 1.04, 0.51, 1.0, -0.53, 0.19, 0.68, 0.16, -1.06, -0.5, 0.84, 1.26, 1.47, -1.55, -1.13, 0.37, 1.13, 0.44, -0.41, -0.77],
[1.21, 0.45, -0.03, -0.4, 0.22, 1.03, 0.15, -0.91, -1.14, 1.41, 0.13, 1.22, -0.71, -1.3, -0.39, 0.76, 0.78, 0.07, -0.61, 0.17],
[0.39, -1.21, -1.81, -0.12, 1.78, 0.92, -0.08, -1.18, -0.78, 0.77, 1.01, 0.29, -0.74, -0.62, 0.35, 0.75, -0.38, -0.64, 0.13, 0.98],
[0.5, -1.72, -1.27, 1.18, -0.14, 0.97, -0.38, -1.04, -0.7, 0.61, 0.74, -0.08, -0.39, 0.3, 0.25, -0.21, -0.84, -0.36, 0.95, 1.43],
[-0.32, -0.07, -0.99, 0.57, 1.44, 0.7, -1.07, -1.04, 1.33, 0.65, 0.21, -0.22, -0.27, 0.55, 0.35, -0.68, -0.96, 0.24, 0.98, 0.84],
[-0.65, -2.63, -0.37, -0.24, 0.67, -0.26, -0.77, 1.14, 1.85, 0.32, -0.89, -0.57, 0.59, 1.09, 0.14, -0.98, -1.24, 0.3, 1.2, 0.52],
[-0.8, 0.46, 0.34, 0.56, 0.18, -0.42, -0.09, 0.72, -1.2, -0.78, -1.08, 0.0, 1.3, 1.18, -0.76, -1.48, -0.58, 0.77, 0.97, 0.14],
[-0.57, 0.69, 0.28, 0.27, -1.63, -0.21, 0.79, 0.72, -0.1, -1.16, -0.85, 0.69, 1.03, 0.33, -0.88, -0.92, 0.16, 0.85, -0.15, -0.63],
[-0.52, -1.02, 0.46, -0.25, 0.72, -0.25, 2.28, 0.89, -0.42, 0.14, -0.25, 0.61, 0.89, -0.04, -0.62, -0.06, 0.71, -0.05, -0.66, -0.42],
[0.36, 0.93, -1.01, 0.01, -1.03, 0.46, 1.41, 0.7, -0.6, -1.31, -1.43, 0.76, 0.42, -0.22, 0.03, 0.24, 0.29, -0.55, -0.9, 0.13],
[1.21, 0.58, 0.64, -1.4, -0.49, 1.04, 1.38, 1.06, -1.01, -0.5, 0.44, 0.5, 1.2, -0.65, 0.3, 0.87, 0.13, -0.95, -0.7, 0.22],
[1.14, 0.45, 0.4, -1.05, 0.21, 1.96, 0.37, -0.44, -0.4, 1.69, 1.96, -0.61, -2.29, -0.12, 1.11, 1.09, -0.2, -1.59, -0.73, 0.76],
[1.22, 0.13, 0.52, -0.91, -1.11, 0.45, -1.44, -0.3, 0.47, 0.48, -0.09, -1.07, -0.87, 0.58, 1.58, 0.32, -1.0, -1.17, -0.01, 0.95],
[0.89, -0.08, -2.14, -0.04, 0.44, -0.04, -0.47, -0.4, 0.74, 0.77, -0.43, -1.22, -0.37, 0.58, 0.99, -0.01, -0.85, -0.39, 0.59, 0.12],
[-0.2, -0.58, 0.02, 0.69, 0.32, -1.86, -2.33, 0.32, 1.31, 0.67, -0.69, -1.51, -0.27, 0.84, 0.61, -0.24, -0.28, -0.09, 0.24, -0.37],
[-0.56, -0.1, 0.92, 1.04, -0.64, -2.7, -0.58, 0.98, 1.42, 0.36, -1.22, -0.8, 0.33, 0.68, 0.09, -0.14, -0.02, 0.63, 0.13, -0.85],
[-0.57, 0.64, 0.98, 0.4, -0.95, -1.2, 0.08, 1.32, 0.52, -0.48, -0.71, 0.08, 0.62, 0.2, -0.87, -0.27, 0.86, 0.96, -0.2, -1.04],
[-0.78, 0.75, 1.21, 0.11, -0.96, -0.58, 0.1, 0.63, 0.04, -0.41, 0.13, 0.83, -0.07, -0.93, -0.86, 0.44, 1.46, 0.89, -1.08, -1.37],
[-0.14, 1.18, 1.0, -1.44, -1.14, -0.33, 1.73, 0.18, -0.35, 0.03, 0.44, 0.62, -0.41, -1.21, -0.45, 2.42, 1.02, -0.01, -1.05, -0.69],
[0.49, 1.16, -0.05, -2.01, -0.34, 0.43, -0.94, -0.38, -1.0, 0.15, 1.13, 0.61, -0.74, -1.05, -0.39, 0.9, 0.76, -0.27, -0.58, 0.19],
[0.85, 0.16, -0.44, -0.29, 0.6, 2.18, 0.72, -1.34, -1.95, 0.88, 1.4, 0.34, -1.39, -1.06, 0.24, 0.84, 0.27, -0.24, -0.36, 0.36],
[0.22, -0.4, -0.54, 0.43, 1.36, 0.32, -0.96, -1.28, -0.02, 1.34, -0.67, -0.53, -1.0, -0.22, 0.6, -0.88, -0.74, -0.43, 0.55, 0.8],
[-0.12, -2.13, -0.24, 0.61, 1.13, 0.08, -2.4, -0.79, 0.62, 0.77, 0.19, -0.53, -0.23, 0.57, 0.58, -0.74, -0.83, 0.27, 1.28, 0.82],
[-0.55, -0.17, -0.24, 2.45, 2.35, -0.19, -0.8, -1.9, 0.42, 0.4, -0.23, -0.15, 0.71, 0.45, -0.35, -2.43, -0.51, 1.01, 1.59, -0.03],
[-1.37, -2.37, 0.42, 1.28, 0.67, -0.84, -0.69, 0.18, 0.43, -0.16, -0.36, -0.06, 0.9, 0.53, -0.74, -1.12, 0.1, 0.9, 0.85, -0.31],
[-1.17, -0.35, 2.15, 0.37, -0.34, 0.8, 0.24, 0.71, 0.11, -1.21, -0.7, 0.73, 1.31, 0.31, -0.9, -1.26, 0.16, 0.97, 0.42, -0.35],
[-0.54, -0.17, 1.61, -0.17, -0.51, 0.19, 1.09, 0.24, -0.92, -1.3, -1.42, 1.31, 1.27, -0.58, -1.25, -0.49, 0.59, 0.63, -0.01, -0.61],
[-0.23, 0.38, 0.0, -0.67, -0.29, -0.89, 0.99, 0.04, -1.17, -0.94, 0.55, 0.87, 0.31, -0.65, -0.57, 0.31, 0.64, -0.52, -0.78, 0.06],
[0.65, 0.55, -1.76, -0.84, -0.33, 1.07, 1.05, -0.25, -1.02, -0.83, 0.41, 0.61, -0.12, -0.35, 0.35, 0.27, -0.26, -1.0, -0.55, 0.85],
[1.24, 0.39, -1.39, -1.18, 0.34, 1.34, -0.55, -0.37, -1.02, -1.35, 0.51, 0.07, -0.32, 0.31, 0.62, 0.44, -0.69, -1.12, 0.01, 0.86],
[0.79, -0.52, -1.34, -0.54, 0.85, 1.16, -0.25, -0.71, -0.12, 0.54, 0.23, -0.45, -0.74, 0.52, 1.16, 0.27, -0.97, -0.8, 0.07, 1.07],
[0.56, -0.68, -0.83, 0.22, 0.39, 1.36, -0.47, -0.08, 0.78, 2.05, -0.83, -1.26, -0.21, 1.21, 1.26, -0.03, -1.45, -0.72, 0.57, 0.83]
],
"data2": [
["Deep deletion", "Amplification", None, "Amplification", None, None, "Deep deletion", None, None, None, None, None, "Deep deletion", None, None, None, None, None, None, None],
["Amplification", None, "Amplification", "Deep deletion", None, None, "Amplification", "Amplification", None, None, None, None, None, None, None, None, None, None, None, None],
["Amplification", None, "Amplification", None, None, None, None, None, None, None, "Amplification", None, None, None, None, None, None, None, None, None],
["Amplification", None, None, "Deep deletion", "Amplification", None, "Deep deletion", None, "Deep deletion", None, None, None, None, None, None, "Amplification", None, None, None, None],
["Amplification", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
["Amplification", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
["Amplification", None, "Deep deletion", "Deep deletion", "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
["Amplification", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
["Deep deletion", None, None, "Amplification", None, None, "Deep deletion", None, "Amplification", None, None, None, None, None, None, None, None, None, None, None],
["Amplification", None, None, "Amplification", None, None, None, None, None, None, None, None, "Amplification", None, None, None, None, None, None, None],
["Amplification", None, None, None, None, None, None, None, None, "Amplification", "Deep deletion", None, None, None, None, None, None, None, None, None],
[None, "Deep deletion", "Deep deletion", None, "Amplification", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, "Deep deletion", None, "Amplification", "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, "Amplification", None, None, None, None, None, None, "Amplification", None, None, None, None, None, None, None, None, None, None, None],
[None, "Deep deletion", None, "Deep deletion", None, None, None, "Amplification", "Amplification", None, None, None, None, None, None, None, None, None, None, None],
[None, "Amplification", None, None, None, None, None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None],
[None, "Amplification", None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, "Deep deletion", None, None, "Amplification", None, "Amplification", None, None, "Amplification", None, None, None, None, None, None, None, None, None, None],
[None, None, "Deep deletion", "Amplification", None, None, None, None, None, None, "Deep deletion", None, None, None, None, None, None, None, None, None],
[None, None, "Amplification", None, None, None, None, "Amplification", None, None, None, None, "Amplification", None, None, None, None, None, None, None],
[None, None, "Amplification", None, None, "Amplification", None, None, None, "Amplification", "Amplification", None, "Deep deletion", None, None, None, None, None, None, None],
[None, None, "Amplification", None, "Deep deletion", None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, "Deep deletion", "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, "Deep deletion", None, None, "Amplification", None, None, None, None, None, None, None, None, "Amplification", None, None, None, None],
[None, None, None, "Deep deletion", None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, "Amplification", "Amplification", None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, None, None, None, None, None, "Deep deletion", None, None, None, None, "Deep deletion", None, None, None, None],
[None, "Deep deletion", None, None, None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, "Amplification", None, "Amplification", "Amplification", None, None, "Deep deletion", None, None, None, None, None, None, None, "Deep deletion", None, None, None, None],
[None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, "Amplification", None, None, "Amplification", None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, "Amplification", None, None, None, None, None, None, None, "Deep deletion", None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, None, "Deep deletion", None, None, "Deep deletion", None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None],
[None, None, None, None, None, "Amplification", None, None, None, "Amplification", None, None, None, None, None, None, None, None, None, None]
],
"data3": [
["", "", "", "", "", "Mutation", "", "Mutation", "", "", "Mutation", "", "", "", "", "Mutation", "", "", "Mutation", ""],
["", "Fusion / SV", "", "", "", "Mutation", "", "", "", "", "", "", "Mutation", "", "Mutation", "", "", "", "", ""],
["", "Mutation", "", "Mutation", "Mutation", "", "", "Mutation", "", "Mutation", "", "Mutation", "Mutation", "", "", "Mutation", "", "", "", ""],
["", "Mutation", "Mutation", "", "", "", "", "Mutation", "", "", "", "", "Fusion / SV", "", "", "", "Mutation", "", "Mutation", ""],
["", "Mutation", "Fusion / SV", "Mutation", "", "", "Mutation", "Mutation", "", "Mutation", "Mutation", "", "", "", "", "", "", "Mutation", "", ""],
["", "Mutation", "", "", "", "", "", "Fusion / SV", "", "", "Mutation", "", "", "", "Mutation", "", "", "", "", ""],
["", "", "", "", "", "", "", "", "", "Mutation", "", "", "", "", "", "Mutation", "Mutation", "", "", ""],
["", "", "Mutation", "", "Mutation", "", "", "", "Mutation", "Fusion / SV", "", "Mutation", "", "", "Mutation", "", "", "", "Mutation", "Mutation"],
["", "", "", "", "Mutation", "Mutation", "", "Fusion / SV", "", "", "", "", "", "", "", "", "", "Mutation", "", ""],
["", "", "", "", "Mutation", "Mutation", "", "", "", "", "", "", "", "", "", "Mutation", "Mutation", "", "", ""],
["", "", "", "", "", "", "", "", "Mutation", "", "", "Mutation", "", "", "", "", "", "Mutation", "", ""],
["Mutation", "", "", "Mutation", "", "", "", "Mutation", "", "Mutation", "", "", "", "Mutation", "", "", "", "", "", "Mutation"],
["Fusion / SV", "", "Mutation", "", "", "", "", "", "", "", "", "", "", "", "Mutation", "", "", "", "", ""],
["Mutation", "", "Fusion / SV", "", "", "Mutation", "", "", "", "", "", "", "Mutation", "", "", "", "", "", "", "Mutation"],
["Mutation", "", "", "", "Mutation", "Fusion / SV", "", "", "", "", "", "", "Mutation", "", "", "", "", "Mutation", "", "Mutation"],
["Mutation", "", "", "Mutation", "Mutation", "", "", "", "", "", "", "Mutation", "", "", "", "", "", "", "", ""],
["Mutation", "", "", "", "", "Mutation", "Mutation", "Mutation", "Mutation", "", "Mutation", "", "Mutation", "", "Mutation", "Fusion / SV", "", "", "", ""],
["Mutation", "", "", "", "", "", "", "Mutation", "Mutation", "", "", "", "", "", "", "", "", "Mutation", "Mutation", ""],
["Mutation", "Mutation", "", "", "", "Mutation", "Fusion / SV", "", "Mutation", "", "", "Mutation", "", "", "", "Mutation", "", "", "", ""],
["Mutation", "Mutation", "", "Mutation", "Mutation", "Fusion / SV", "Mutation", "", "", "", "Mutation", "Mutation", "", "Mutation", "", "", "Mutation", "Mutation", "Mutation", "Mutation"],
["Mutation", "Mutation", "", "Mutation", "", "", "", "Mutation", "", "", "", "", "", "Mutation", "", "", "Mutation", "", "", ""],
["Fusion / SV", "Mutation", "", "", "", "", "", "", "", "", "Fusion / SV", "", "", "", "Mutation", "", "", "", "", ""],
["Fusion / SV", "Fusion / SV", "", "", "Mutation", "", "", "", "", "Fusion / SV", "", "", "Mutation", "", "", "", "Mutation", "", "", ""],
["Mutation", "Mutation", "Mutation", "Mutation", "", "", "", "", "", "", "", "", "", "Mutation", "", "", "", "", "Mutation", ""],
["Fusion / SV", "Mutation", "Mutation", "Mutation", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""],
["Mutation", "Mutation", "Mutation", "Mutation", "", "Mutation", "", "", "Mutation", "", "Mutation", "", "", "", "", "Mutation", "", "", "", ""],
["Mutation", "Mutation", "Fusion / SV", "Mutation", "", "", "", "", "", "Mutation", "", "", "", "", "", "", "Mutation", "Mutation", "", ""],
["Mutation", "", "Mutation", "", "", "", "", "Fusion / SV", "Mutation", "", "", "Mutation", "", "", "", "", "", "", "", ""],
["Mutation", "", "Mutation", "", "", "", "", "Fusion / SV", "", "", "", "Mutation", "", "Mutation", "", "", "", "", "Mutation", "Mutation"],
["Mutation", "", "Mutation", "", "Mutation", "", "", "", "", "Mutation", "", "", "", "", "Mutation", "", "", "", "", ""],
["Mutation", "", "", "", "Mutation", "Mutation", "", "", "", "", "", "", "", "", "Mutation", "", "", "", "", "Mutation"],
["", "", "Fusion / SV", "", "Mutation", "Mutation", "", "", "Mutation", "Mutation", "", "Mutation", "", "", "", "", "", "", "Mutation", ""],
["", "", "", "", "", "", "Mutation", "", "", "", "", "Mutation", "", "Mutation", "", "", "Mutation", "Mutation", "", "Mutation"],
["", "", "", "Mutation", "", "", "", "", "Mutation", "", "", "", "", "", "Mutation", "", "", "", "", ""],
["", "Fusion / SV", "", "Mutation", "Mutation", "", "Mutation", "", "", "Mutation", "Mutation", "", "Mutation", "Mutation", "Mutation", "", "", "Mutation", "", ""],
["", "Mutation", "", "", "Mutation", "Mutation", "Mutation", "", "", "", "", "", "", "", "", "", "Mutation", "", "", "Mutation"],
["", "Mutation", "Fusion / SV", "", "", "", "Mutation", "", "", "", "", "Mutation", "", "Mutation", "", "", "", "", "", ""],
["", "", "", "", "Fusion / SV", "", "", "", "", "", "", "Mutation", "", "", "", "", "", "", "", ""],
["", "", "Mutation", "Mutation", "", "", "", "", "", "", "", "Mutation", "", "Mutation", "Mutation", "", "", "", "", "Mutation"],
["", "", "", "", "Fusion / SV", "Mutation", "", "Mutation", "", "Mutation", "", "", "", "Mutation", "", "", "Mutation", "", "Mutation", ""],
["", "", "", "", "", "", "Mutation", "", "Fusion / SV", "", "Mutation", "", "", "Mutation", "", "", "", "Mutation", "Mutation", ""]
]
}
},
config = {
"graphType": "Heatmap",
"oncoprintCNA": "data2",
"overlaysThickness": 100,
"oncoprintPresorted": True,
"oncoprintMUT": "data3"
},
width = 900,
height = 650
)
# 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 = "oncoprint5",
data = {
"y": {
"vars": ["T39", "T30", "T18", "T25", "T29", "T31", "T28", "T15", "T13", "T05", "T12", "T03", "T14", "T02", "T09", "T17", "T10", "T21", "T34", "T01", "T26", "T22", "T06", "T19", "T07", "T16", "T35", "T08", "T11", "T24", "T32", "T36", "T41", "T04", "T40", "T37", "T20", "T33", "T27", "T38", "T23"],
"smps": ["EGFR", "TP53", "MYC", "PTEN", "BRCA1", "BRCA2", "PIK3CA", "RB1", "AKT1", "KRAS", "MTOR", "ZNF140", "CCND1", "ZNF171", "ZNF096", "CDKN2A", "ZNF042", "ZNF089", "ZNF108", "ZNF051"],
"data": [
[-1.15, 2.25, 0.27, 0.28, -1.09, 0.31, -0.4, 0.55, -0.56, -0.78, 0.09, 0.71, -1.57, -0.72, -0.17, 0.84, 0.85, -0.28, -1.55, -0.62],
[2.2, 1.18, 1.28, -2.33, -0.49, 0.29, 2.09, 1.4, -0.43, 0.08, 0.18, -0.05, -0.81, -0.66, 0.59, 1.46, 0.16, -1.17, -1.29, 0.05],
[2.63, 0.99, 1.06, -1.2, -0.29, 0.55, 0.32, -0.23, 0.09, 0.4, 1.83, -0.45, -1.09, -0.23, 0.69, 1.03, -0.13, -1.13, -0.63, 0.63],
[2.61, -0.02, -0.76, -1.69, 1.72, 0.43, -1.54, -0.82, -1.04, 1.1, 0.48, -0.8, -0.94, -0.17, 1.07, 2.08, -0.35, -0.65, 0.2, 0.3],
[1.61, -0.36, -0.28, 0.55, 0.81, -0.58, -1.2, -0.43, 1.02, 1.37, 0.21, -1.46, -0.97, 0.43, 1.0, 0.33, -0.26, -0.41, 0.33, 0.17],
[1.05, -0.39, 0.5, 0.71, 0.21, -1.0, -1.14, 0.21, 1.5, 0.61, -0.63, -1.06, -0.17, 0.73, 0.56, -0.62, -0.38, 0.52, 0.71, -0.21],
[0.63, -0.64, -0.59, -0.23, -1.36, -1.14, -0.66, 0.24, 0.92, 0.21, -0.59, -0.28, 0.56, 0.04, -0.6, -0.65, 0.38, 1.25, 0.7, -1.19],
[-0.01, -0.01, 1.28, 1.01, -0.32, -1.45, -0.51, 0.59, 0.55, -0.15, -0.14, 0.06, 0.39, -0.34, -0.99, -0.29, 1.15, 0.96, -0.17, -1.27],
[-2.21, 0.64, 1.41, 1.96, -0.92, -0.73, -1.08, 0.54, 1.28, -0.82, 0.01, 0.85, 0.42, -0.77, -0.98, -0.26, 1.06, 0.84, -0.42, -0.92],
[1.08, 1.04, 0.51, 1.0, -0.53, 0.19, 0.68, 0.16, -1.06, -0.5, 0.84, 1.26, 1.47, -1.55, -1.13, 0.37, 1.13, 0.44, -0.41, -0.77],
[1.21, 0.45, -0.03, -0.4, 0.22, 1.03, 0.15, -0.91, -1.14, 1.41, 0.13, 1.22, -0.71, -1.3, -0.39, 0.76, 0.78, 0.07, -0.61, 0.17],
[0.39, -1.21, -1.81, -0.12, 1.78, 0.92, -0.08, -1.18, -0.78, 0.77, 1.01, 0.29, -0.74, -0.62, 0.35, 0.75, -0.38, -0.64, 0.13, 0.98],
[0.5, -1.72, -1.27, 1.18, -0.14, 0.97, -0.38, -1.04, -0.7, 0.61, 0.74, -0.08, -0.39, 0.3, 0.25, -0.21, -0.84, -0.36, 0.95, 1.43],
[-0.32, -0.07, -0.99, 0.57, 1.44, 0.7, -1.07, -1.04, 1.33, 0.65, 0.21, -0.22, -0.27, 0.55, 0.35, -0.68, -0.96, 0.24, 0.98, 0.84],
[-0.65, -2.63, -0.37, -0.24, 0.67, -0.26, -0.77, 1.14, 1.85, 0.32, -0.89, -0.57, 0.59, 1.09, 0.14, -0.98, -1.24, 0.3, 1.2, 0.52],
[-0.8, 0.46, 0.34, 0.56, 0.18, -0.42, -0.09, 0.72, -1.2, -0.78, -1.08, 0.0, 1.3, 1.18, -0.76, -1.48, -0.58, 0.77, 0.97, 0.14],
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"overlaysThickness": 100,
"oncoprintPresorted": True,
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},
width = 900,
height = 650
)
)
