# Questions tagged [heatmap]

A heatmap is a visual representation of data where values in a matrix is represented as colors, often after a re-ordering of the rows and columns to emphasize similarities.

55 questions
Filter by
Sorted by
Tagged with
59 views

### Is there a statistical test to compare two heatmaps/response surfaces or two curves?

I am conducting a series of experiments in which I analyse the effect of the order of treatment of bacterial cells with different concentrations of two compounds (Drug 1 and Drug 2). The values in the ...
13 views

### Spatial autocorrelation weight matrix for heatmaps

I am not an advanced mathematician and I'm very new to spatial autocorrelation. So I apologize if my question seems primitive in any way. I'm looking for ways to quantify the distribution similarity ...
164 views

### A correlation heatmap with only negative values?

Putting aside the fact that this are, on the whole, fairly weak correlations, does this correlation heatmap of products used by various users, which has ONLY negative values, seem strange to anyone? I'...
30 views

### Turning heatmap into clusters - Classification

Assume that you having a heatmap that looks like this. The goal is to classify all the "dot" inside the image. How can that be done? The assumptions of the image: The image has always black ...
• 425
277 views

### How to interpret result of cube root transform applied to fractional numbers?

I would like to use the cube root transform on data in order to preserve the sign of the original data and 0 values. The data are percent differences between control and treatment groups, (treatment -...
4k views

### Scaling heatmaps in R by row and column

Hopefully, this post is appropriate for CV and won't be closed. I have a non-symmetric matrix $M_{K \times K}$ comparing a new statistic, $\delta$, my colleagues and I developed and tested on a ...
• 1,579
1 vote
33 views

### Compare location data of passes made by two teams in the same game in a coordinate system

I have two sets of data (courtesy of Statsbomb), where each contains the x,y location of where passes occured during a football game as well as the minute of the event for the two different teams. My ...
• 337
1 vote
63 views

### Optimal number of clusters in gene expression data

I'm clustering genes on gene expression data. Here's a hierarchically clustered heatmap using ward linkage and Euclidean distance It clearly shows there are 5 or 6 clusters. Now when I evaluate their ...
166 views

### Finding correlations between categories using Correlations matrix and heatmap with dendrogram

I have a dataset with 5000 obs grouped by category: 1: science 0.5: philosophy -0.5: medicine -1: law I would like to run some statistics to find correlations among variables within the groups, for ...
• 85
1 vote
34 views

### How could I even try to analyze map data? [closed]

I have a situation where I'm trying to analyze how users interact with maps. Here's an example to illustrate: Below is an image of Google maps after searching for Chicago, IL pizza. Now, say that I ...
• 31
1 vote
257 views

### Is there a way to filter a heatmap based on relevance?

I'm currently working with ComplexHeatmap and a very large dataset from RNAseq (~13,000 genes/columns). The heatmap output (based off of clustering) at the moment contains so many columns it's ...
68 views

### Visualize multiple rejection reasons

Goal: Visualize why loans are rejected which can be due to multiple reasons. A loan is either rejected or accepted. Any rejection is caused by one or more rejection reasons. There is a list of ...
• 267
2k views

### What is the difference between a class activation map and a saliency map for convolutional neural networks?

I am researching attribution methods in computer vision literature to better understand how a CNN model arrives at its predictions. I have come across the terms ...
• 1,030
1 vote
222 views

...
• 1,323
931 views

### How to construct this "prediction heatmap" assuming OLS (worked out example)

The following visual certainly delivers in terms of eye candy: There was no details on the model specification, but let's just assume its something like: price = \beta_{0} + \beta_{1} x_{surface} +...
1 vote
20 views

### Create heatmaps in R from local coordinates [closed]

I have a player movement dataset which has 2D player location coordinates every second. I'm looking to create a heatmap of where the player stay longer. I've seen a few answers on creating ...
• 13
1 vote
16 views

### Seeking suggestions for data display for table with supercategories, sections and bold-heatmap? dartboard?

I'm trying to visually display the results of a table where we used vote counting to categorically summarize (in many ways) multiple outcomes from a list of studies and compare to how they were ...
1 vote
417 views

### Autoencoder on heat maps

I have time sequences of 2D heat maps. For different people I have heat maps over time. For each person I have around 720 heat maps and in total around 50'000 heat maps. Now, I would like to train ...
• 1,814
1 vote
60 views

### Visualizing speed and acceleration of typing (smartphone keyboard)

I have a dataset of smartphone keyboard recordings. Each sample consists of the pressed key on the keyboard (e.g. 'a') and the timestamp. From this data I can compute the speed of typing (speed ...
• 1,814
3k views

### Statistically compare similarity between images

I have two images/heatmaps (2d matrix) of identical size. I need to statistically compare the similarity between the two. With 'similarity', I mean that high and low values of one image appear in ...
• 165
3k views

### Hierarchical clustering dendrogram on a distance matrix

When computing hierarchical clustering over a data matrix, a dissimilarity matrix is first computed in order to build the tree (dendrogram). For example: ...
• 1,114
40 views

### Finding the effect of nodes on a density heatmap

Let's say I have a geo-tagged dataset of all payment transactions for businesses in a city. I know whether each payment is made by cash or card, and have made a heatmap of where in the city the ...
• 399
173 views

### Comparing 3 raster maps of continuous surface data in R

I have 3 maps representing spatial distribution in hunting pressure. These maps were derived using different methods and I am now interested in comparing them to assess how they might differ/agree ...
59k views

### How can one interpret a heat map plot

I am doing a stats assignment in python and during my preliminary data analysis I created a heatmap plot and would like to be able to explain the correlation among the variables. However, I don't ...
• 83
647 views

### Statistical test for determining hot spot in a heat map

I'm analyzing high through proteomic data and have several thousand 5x5 matrices, where in each matrix the rows and columns refer to different biological conditions, and each cell refers to gene ...
• 41
3k views

### What is a probability heat map?

What is a probability heat map? In general, what is a heat map? Many papers on neural networks use probability heat maps for visualisation. My understanding is that heat maps are plots of (typically ...
• 163
30 views

### Which distance function do you have to use for miRNA expression data?

For a set of miRNA gene expression data from different cancer patients I produced some heatmaps with R. The goal is to examine which miRNAs are up/downregulated depending on different parameters (...
34 views

### What's it called for a heatmap with things that aren't square and test points are all over it?

I'm trying to make a visualization of my home states' temperature ranges, but I'm not sure what the name of the plot I want is called. It's like a heatmap, but the test points with a value are located ...
• 201
281 views

### How to normalize three variables into one ordinal scale?

I have three same scaled variables (Strategy 1: Stay, Strategy 2: Move, Strategy 3: Move far) which I want to compare in a heatmap for different locations. For each strategy an operator earns a ...
• 3
68 views

### How can I rate the predictive power of a function through a heatmap?

Context: I use a certain function that is supposed to estimate the possibility of an event "B" to occur in a given area, following the occurence of event "A". The input is a map of the area, and the ...
• 43
15k views

### Are heat maps "one of the least effective types of data visualization"?

Question: When (for what types of data visualization problems) are heat maps most effective? (In particular, more effective than all other possible visualization techniques?) When are heat maps least ...
• 6,309
1 vote
2k views

### genes significantly different compared to other groups

I am trying to compare genes that differ significantly between groups and only plot them in the heatmap. I am using R and its libraries ComplexHeatmap and cirlize. The sample of the data that I have ...
• 4,515
553 views

### Kriging variance results

I'm quite a newb at statistics and interpolation, and I cannot understand how to interpret the error estimation computed by Kriging. For example, I performed kriging on temperature values (Celsius ...
1 vote
579 views

### Preparing Data for Convolutional Neural Network Training

I am working on a project that involves creating a set of n heat maps that will become the training data for a CNN to perform a binary classification. As of now, I have 1,000 heat maps with 649 in the ...
• 312
236 views

### Heatmap based on gene expression trend [closed]

Can anybody guide me on the R code for the following problem? My data contains expression values of Genes A, B, C, D, E, F, G, H, and I in a time course study for two time steps, 48 and 72 hours, ...
555 views

### Which statistical analysis and graphical representation are appropriate for longitudinal bacterial quantification data?

Recently I have conducted a microbiological experiment on carriage pattern of bacteria in a certain group of professional people over a week. It would be very helpful for me if somebody suggest which ...
• 61
1k views

### Showing a correlation and its p-value as a color

I want to convey in a heatmap how well are some correlations $[-1, 1]$ with its p-value $[0, 1]$. To normalize the plotting, the resulting numbers must be between $-1$ and $1$ and the sign must be the ...
• 595
594 views

### Why does the heatmap of this gene expression data don't show a decent clustering here?

The heatmap has samples in columns and probesets/features in the rows. The genes are already selected based on a very low p-value threshold using 2 sample t-test on the two phenotypic subgroups of the ...
• 277
1 vote
765 views

### Do heights between branches in R's heatmap dendrogram reflect true distances?

We are trying to interpret a heatmap that looks like this: ... and plotted with this plotting code: ...
• 111
1k views

### Row Correlation Heatmap Pandas

I'm trying to find any relationship/patterns between a large number of rows in a dataset (~2000) and I'm thinking of using a correlation heatmap. However, after transforming the df using ...
1 vote
596 views

### How to best describe a bunch of 2D histograms/distributions?

For chords of several music genres, I have subjective ratings from subjects that show how pleasant they found each chord (x axis below) and also how consonant (y axis). A scatter plot (or rather a ...
• 2,302
1k views

### R/MASS kde2d and bandwidth.nrd

First off, I didn't know whether to post this here or on SO. I tossed a coin and ended here. Second, I'm trying to get a grip on the kde2d function in the MASS ...
2k views

### Making a heatmap understandable when printed in black ink

What are some good ways to make a heatmap understandable when printed in black ink? (without having to butcher the color version too much, as some reader might have some color printer, or read on the ...
• 47.1k
108 views

### cross validating time series model

I'm evaluating a model predicting clickrate. I have series of clicks and impressions. At the moment I'm evaluating a particular feature X. It's a categorical ...
1 vote
52 views

### Ranking a negative correlation as equal to a positive correlation on a column-by-column basis for distance measures

I am very new to r, but have managed to muddle together a functional script to tackle data from a screen I am working on. I have a list of mutants of genes in a signaling network and values (OD550) ...
• 11
176 views

### Reading a simplex heatmap [duplicate]

I have trouble reading the following simplex heatmap. Description of the figure: Consider a three-label classification problem. Simplex corners indicate where one label has very high probability, ...
• 133
1k views

### Best way to visualize data with two keys and many rows in R (heatmap, mosaic plot, treemap, ggplot)

I have been wrestling with the problem of creating some type of visualization for my data. I have two keys (used in data table to create the data) that are intervals. I constructed the intervals ...
• 48
1 vote
120 views

### How to calculate third variable dependence on x,y variables and visualise with heatmap using binning?

I have a dataframe with an X and Y column and a third column with an additional variable (let's call it "ABC"). I would like to create a heatmap that visualizes how ABC depends on the X and Y ...
• 848
1 vote