Interactive heatmap at scale
Heatmap graphs provide a visual representation of data using color variations to represent different values. They are incredibly useful for identifying patterns, trends, and outliers in datasets. Commonly used in various fields, from geographical analysis to website usability studies, heatmaps offer an intuitive way to understand complex data. Creating effective heatmaps involves selecting the appropriate color scheme and scaling to highlight meaningful differences. Interactive heatmaps further enhance analysis by allowing users to zoom, pan, and explore data points in detail. This makes them powerful tools for data-driven decision making across numerous disciplines.
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"Normal",
"Normal",
"Normal",
"Normal",
"Normal",
"Normal",
"Normal"
],
"Batch" : [
"B2",
"B2",
"B3",
"B3",
"B1",
"B1",
"B3",
"B3",
"B1",
"B1",
"B3",
"B2",
"B1",
"B3",
"B1",
"B2",
"B2",
"B2",
"B1",
"B1",
"B3",
"B3",
"B3",
"B2",
"B3",
"B1",
"B2",
"B3",
"B1",
"B1",
"B1",
"B2",
"B3",
"B1",
"B2",
"B2",
"B3",
"B1",
"B2",
"B1",
"B1",
"B3",
"B1",
"B1",
"B2",
"B2",
"B1",
"B3",
"B3",
"B3",
"B1",
"B3",
"B1",
"B2",
"B3",
"B1",
"B3",
"B1",
"B1",
"B3",
"B2",
"B2",
"B1",
"B1",
"B2",
"B2",
"B2",
"B3",
"B2",
"B2",
"B3",
"B3",
"B2",
"B1",
"B3",
"B2",
"B3",
"B2",
"B2",
"B1"
]
},
"z" : {
"Pathway" : [
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Cell cycle",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Immune",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism",
"Metabolism"
]
}
}
// Create the configuration for the graph
var config = {
"graphType" : "Heatmap",
"title" : "Interactive heatmap at scale",
"subtitle" : "150 genes x 80 samples = 12,000 expression values",
"samplesClustered" : true,
"variablesClustered" : true,
"colorSpectrum" : [
"navy",
"white",
"firebrick3"
],
"showSmpDendrogram" : true,
"showVarDendrogram" : true,
"heatmapIndicatorPosition" : "right"
}
// 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-heatmap18-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-heatmap18-smp.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-heatmap18-var.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
data=y,
smpAnnot=x,
varAnnot=z,
colorSpectrum=list("navy", "white", "firebrick3"),
graphType="Heatmap",
heatmapIndicatorPosition="right",
samplesClustered=TRUE,
showSmpDendrogram=TRUE,
showVarDendrogram=TRUE,
subtitle="150 genes x 80 samples = 12,000 expression values",
title="Interactive heatmap at scale",
variablesClustered=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 = "heatmap18",
data = {
"y": {
"vars": ["Gene1", "Gene2", "Gene3", "Gene4", "Gene5", "Gene6", "Gene7", "Gene8", "Gene9", "Gene10", "Gene11", "Gene12", "Gene13", "Gene14", "Gene15", "Gene16", "Gene17", "Gene18", "Gene19", "Gene20", "Gene21", "Gene22", "Gene23", "Gene24", "Gene25", "Gene26", "Gene27", "Gene28", "Gene29", "Gene30", "Gene31", "Gene32", "Gene33", "Gene34", "Gene35", "Gene36", "Gene37", "Gene38", "Gene39", "Gene40", "Gene41", "Gene42", "Gene43", "Gene44", "Gene45", "Gene46", "Gene47", "Gene48", "Gene49", "Gene50", "Gene51", "Gene52", "Gene53", "Gene54", "Gene55", "Gene56", "Gene57", "Gene58", "Gene59", "Gene60", "Gene61", "Gene62", "Gene63", "Gene64", "Gene65", "Gene66", "Gene67", "Gene68", "Gene69", "Gene70", "Gene71", "Gene72", "Gene73", "Gene74", "Gene75", "Gene76", "Gene77", "Gene78", "Gene79", "Gene80", "Gene81", "Gene82", "Gene83", "Gene84", "Gene85", "Gene86", "Gene87", "Gene88", "Gene89", "Gene90", "Gene91", "Gene92", "Gene93", "Gene94", "Gene95", "Gene96", "Gene97", "Gene98", "Gene99", "Gene100", "Gene101", "Gene102", "Gene103", "Gene104", "Gene105", "Gene106", "Gene107", "Gene108", "Gene109", "Gene110", "Gene111", "Gene112", "Gene113", "Gene114", "Gene115", "Gene116", "Gene117", "Gene118", "Gene119", "Gene120", "Gene121", "Gene122", "Gene123", "Gene124", "Gene125", "Gene126", "Gene127", "Gene128", "Gene129", "Gene130", "Gene131", "Gene132", "Gene133", "Gene134", "Gene135", "Gene136", "Gene137", "Gene138", "Gene139", "Gene140", "Gene141", "Gene142", "Gene143", "Gene144", "Gene145", "Gene146", "Gene147", "Gene148", "Gene149", "Gene150"],
"smps": ["S001", "S002", "S003", "S004", "S005", "S006", "S007", "S008", "S009", "S010", "S011", "S012", "S013", "S014", "S015", "S016", "S017", "S018", "S019", "S020", "S021", "S022", "S023", "S024", "S025", "S026", "S027", "S028", "S029", "S030", "S031", "S032", "S033", "S034", "S035", "S036", "S037", "S038", "S039", "S040", "S041", "S042", "S043", "S044", "S045", "S046", "S047", "S048", "S049", "S050", "S051", "S052", "S053", "S054", "S055", "S056", "S057", "S058", "S059", "S060", "S061", "S062", "S063", "S064", "S065", "S066", "S067", "S068", "S069", "S070", "S071", "S072", "S073", "S074", "S075", "S076", "S077", "S078", "S079", "S080"],
"data": [
[1.865, 1.064, 1.39, 1.757, 1.233, 1.741, 1.857, 1.821, 1.496, 2.156, 2.335, 1.993, 1.309, 2.239, 1.499, 2.327, 1.157, 2.349, 1.788, 1.051, 1.612, 1.832, 1.964, 1.211, 1.136, 1.92, 1.52, 1.941, 2.256, 0.811, 1.953, 2.535, 1.621, 1.314, 2.251, 1.952, 2.338, 1.593, 0.911, 1.734, -0.987, -0.255, -0.604, -1.699, -1.437, -0.19, -0.312, -1.104, -0.721, -0.453, -0.439, -0.194, -0.566, -0.777, -0.875, -0.087, -2.071, -0.803, -0.7, -1.575, -0.52, -1.111, -0.203, -0.795, -0.319, 0.011, -0.49, -1.245, -1.629, 0.332, -0.787, -1.133, -0.633, -0.835, -0.209, -0.7, -0.712, -1.149, -0.438, -1.34],
[2.2, 2.714, 0.885, 0.32, 2.17, 3.329, 1.199, 1.05, 2.153, 1.296, 1.496, 1.591, 2.119, 1.557, 1.967, 1.694, 1.293, 1.608, 1.23, 1.804, 1.126, 1.144, 2.674, 1.768, 1.768, 2.107, 1.547, 1.663, 2.055, 1.969, 1.104, 2.3, 1.446, 1.166, 1.26, 1.566, 2.776, 1.095, 1.896, 0.517, -0.721, -0.18, -0.862, -1.098, -0.581, -0.3, -0.322, 0.463, -0.594, -1.075, -0.796, -0.763, -0.655, -0.738, -0.616, -1.723, -0.222, -1.065, -1.424, -0.337, 0.07, -0.424, -0.623, -1.279, 1.003, -0.192, -1.404, -1.188, -0.668, -1.653, -0.619, -0.995, 0.016, -0.143, -2.347, -0.695, -1.69, -0.054, -0.619, -0.391],
[1.161, 2.897, 3.012, 1.161, 2.024, 1.396, 1.786, 1.041, 2.92, 1.218, 1.622, 2.101, 1.411, 1.656, 1.462, 1.72, 1.098, 1.537, 1.676, 1.6, 1.834, 1.624, 2.252, 1.606, 1.718, 1.401, 1.484, 1.041, 2.111, 1.114, 1.352, 2.016, 2.042, 1.56, 0.588, 2.052, 1.956, 0.953, 2.262, 1.379, -1.396, -0.663, -0.827, -0.598, -1.683, 0.367, -1.082, -1.644, -0.349, -0.933, -0.525, -0.924, -0.756, -0.573, -1.168, -0.313, -1.002, -1.242, -0.674, -0.453, -0.857, -1.238, -0.348, -1.776, -1.339, -0.696, -1.537, -0.703, -0.753, -0.181, -1.269, -1.096, -0.52, -2.195, 1.14, -1.139, -1.158, -0.203, -0.744, -1.788],
[2.176, 2.313, 1.53, 1.631, 2.092, 1.255, 2.063, 1.92, 1.395, 0.965, 1.665, 1.275, 2.401, 1.886, 2.269, 1.881, 1.958, 1.33, 2.201, 2.871, 1.614, 1.444, 1.705, 1.511, 1.379, 1.883, 1.625, 2.663, 1.8, 1.994, 2.371, 1.62, 2.662, 1.42, 1.315, 1.58, 1.731, 0.959, 1.779, 0.8, 0.115, -0.769, -1.105, -1.265, -0.951, -0.854, -1.347, -1.272, -0.832, -1.032, -0.156, -0.037, -0.71, -0.436, -1.521, -0.338, -0.738, -0.429, 0.24, -2.089, -0.563, -1.379, -0.365, -1.508, -1.017, -0.598, -0.352, -0.675, -1.196, -1.052, -0.189, -0.723, -1.73, -0.214, -0.47, -0.196, -0.922, -0.223, -1.357, -0.378],
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"x": {
"Condition": ["Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Tumor", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal", "Normal"],
"Batch": ["B2", "B2", "B3", "B3", "B1", "B1", "B3", "B3", "B1", "B1", "B3", "B2", "B1", "B3", "B1", "B2", "B2", "B2", "B1", "B1", "B3", "B3", "B3", "B2", "B3", "B1", "B2", "B3", "B1", "B1", "B1", "B2", "B3", "B1", "B2", "B2", "B3", "B1", "B2", "B1", "B1", "B3", "B1", "B1", "B2", "B2", "B1", "B3", "B3", "B3", "B1", "B3", "B1", "B2", "B3", "B1", "B3", "B1", "B1", "B3", "B2", "B2", "B1", "B1", "B2", "B2", "B2", "B3", "B2", "B2", "B3", "B3", "B2", "B1", "B3", "B2", "B3", "B2", "B2", "B1"]
},
"z": {
"Pathway": ["Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Cell cycle", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Immune", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism", "Metabolism"]
}
},
config = {
"graphType": "Heatmap",
"title": "Interactive heatmap at scale",
"subtitle": "150 genes x 80 samples = 12,000 expression values",
"samplesClustered": True,
"variablesClustered": True,
"colorSpectrum": ["navy", "white", "firebrick3"],
"showSmpDendrogram": True,
"showVarDendrogram": True,
"heatmapIndicatorPosition": "right"
},
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 = "heatmap18",
data = {
"y": {
"vars": ["Gene1", "Gene2", "Gene3", "Gene4", "Gene5", "Gene6", "Gene7", "Gene8", "Gene9", "Gene10", "Gene11", "Gene12", "Gene13", "Gene14", "Gene15", "Gene16", "Gene17", "Gene18", "Gene19", "Gene20", "Gene21", "Gene22", "Gene23", "Gene24", "Gene25", "Gene26", "Gene27", "Gene28", "Gene29", "Gene30", "Gene31", "Gene32", "Gene33", "Gene34", "Gene35", "Gene36", "Gene37", "Gene38", "Gene39", "Gene40", "Gene41", "Gene42", "Gene43", "Gene44", "Gene45", "Gene46", "Gene47", "Gene48", "Gene49", "Gene50", "Gene51", "Gene52", "Gene53", "Gene54", "Gene55", "Gene56", "Gene57", "Gene58", "Gene59", "Gene60", "Gene61", "Gene62", "Gene63", "Gene64", "Gene65", "Gene66", "Gene67", "Gene68", "Gene69", "Gene70", "Gene71", "Gene72", "Gene73", "Gene74", "Gene75", "Gene76", "Gene77", "Gene78", "Gene79", "Gene80", "Gene81", "Gene82", "Gene83", "Gene84", "Gene85", "Gene86", "Gene87", "Gene88", "Gene89", "Gene90", "Gene91", "Gene92", "Gene93", "Gene94", "Gene95", "Gene96", "Gene97", "Gene98", "Gene99", "Gene100", "Gene101", "Gene102", "Gene103", "Gene104", "Gene105", "Gene106", "Gene107", "Gene108", "Gene109", "Gene110", "Gene111", "Gene112", "Gene113", "Gene114", "Gene115", "Gene116", "Gene117", "Gene118", "Gene119", "Gene120", "Gene121", "Gene122", "Gene123", "Gene124", "Gene125", "Gene126", "Gene127", "Gene128", "Gene129", "Gene130", "Gene131", "Gene132", "Gene133", "Gene134", "Gene135", "Gene136", "Gene137", "Gene138", "Gene139", "Gene140", "Gene141", "Gene142", "Gene143", "Gene144", "Gene145", "Gene146", "Gene147", "Gene148", "Gene149", "Gene150"],
"smps": ["S001", "S002", "S003", "S004", "S005", "S006", "S007", "S008", "S009", "S010", "S011", "S012", "S013", "S014", "S015", "S016", "S017", "S018", "S019", "S020", "S021", "S022", "S023", "S024", "S025", "S026", "S027", "S028", "S029", "S030", "S031", "S032", "S033", "S034", "S035", "S036", "S037", "S038", "S039", "S040", "S041", "S042", "S043", "S044", "S045", "S046", "S047", "S048", "S049", "S050", "S051", "S052", "S053", "S054", "S055", "S056", "S057", "S058", "S059", "S060", "S061", "S062", "S063", "S064", "S065", "S066", "S067", "S068", "S069", "S070", "S071", "S072", "S073", "S074", "S075", "S076", "S077", "S078", "S079", "S080"],
"data": [
[1.865, 1.064, 1.39, 1.757, 1.233, 1.741, 1.857, 1.821, 1.496, 2.156, 2.335, 1.993, 1.309, 2.239, 1.499, 2.327, 1.157, 2.349, 1.788, 1.051, 1.612, 1.832, 1.964, 1.211, 1.136, 1.92, 1.52, 1.941, 2.256, 0.811, 1.953, 2.535, 1.621, 1.314, 2.251, 1.952, 2.338, 1.593, 0.911, 1.734, -0.987, -0.255, -0.604, -1.699, -1.437, -0.19, -0.312, -1.104, -0.721, -0.453, -0.439, -0.194, -0.566, -0.777, -0.875, -0.087, -2.071, -0.803, -0.7, -1.575, -0.52, -1.111, -0.203, -0.795, -0.319, 0.011, -0.49, -1.245, -1.629, 0.332, -0.787, -1.133, -0.633, -0.835, -0.209, -0.7, -0.712, -1.149, -0.438, -1.34],
[2.2, 2.714, 0.885, 0.32, 2.17, 3.329, 1.199, 1.05, 2.153, 1.296, 1.496, 1.591, 2.119, 1.557, 1.967, 1.694, 1.293, 1.608, 1.23, 1.804, 1.126, 1.144, 2.674, 1.768, 1.768, 2.107, 1.547, 1.663, 2.055, 1.969, 1.104, 2.3, 1.446, 1.166, 1.26, 1.566, 2.776, 1.095, 1.896, 0.517, -0.721, -0.18, -0.862, -1.098, -0.581, -0.3, -0.322, 0.463, -0.594, -1.075, -0.796, -0.763, -0.655, -0.738, -0.616, -1.723, -0.222, -1.065, -1.424, -0.337, 0.07, -0.424, -0.623, -1.279, 1.003, -0.192, -1.404, -1.188, -0.668, -1.653, -0.619, -0.995, 0.016, -0.143, -2.347, -0.695, -1.69, -0.054, -0.619, -0.391],
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}
},
config = {
"graphType": "Heatmap",
"title": "Interactive heatmap at scale",
"subtitle": "150 genes x 80 samples = 12,000 expression values",
"samplesClustered": True,
"variablesClustered": True,
"colorSpectrum": ["navy", "white", "firebrick3"],
"showSmpDendrogram": True,
"showVarDendrogram": True,
"heatmapIndicatorPosition": "right"
},
width = 600,
height = 600
)
)
