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.
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Distance measures for row ordering of a sparse heatmap with discrete row data
I have a list of protein indexes. Each protein can be either (i) a feature component F in a feature group G (in which case the index is included in the list) or (ii) a background component B (in ...
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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 ...
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Attention Scores in Seq2seq sorting example
This question is about the interpretation of the additive attention (Bahdanau) scores in a seq2seq problem concerning the sorting of an input numerical sequence.
I have a LSTM Encoder/Decoder model ...
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prepare two cols for heatmap comparison
Caveat, I admit being not well versed in transformation.
I have two columns of gene with counts of 1) cancer association, 2) other diseases. The first col ranges from 0-6, the second from 2-980.
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Modeling probability of action as a function of spatial distance
I'm trying to model how people interact with pins on a map, like the one below that shows pizza restaurants in the city of Chicago:
I'm envisioning people interacting with this map in terms of "...
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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 ...
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1answer
84 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 ...
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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
...
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661 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 ...
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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} +...
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1answer
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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 ...
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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 ...
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290 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 ...
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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 ...
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1answer
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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 ...
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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:
...
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1answer
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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 ...
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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 ...
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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 ...
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318 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 ...
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1answer
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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 ...
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1answer
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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 (...
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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 ...
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209 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 ...
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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 ...
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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 ...
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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 ...
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1answer
326 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 ...
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1answer
564 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 ...
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1answer
210 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, ...
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480 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 ...
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496 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 ...
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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:
...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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) ...
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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, ...
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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 ...
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1answer
97 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 ...
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Quality Control Heat Map
I have data for people about their quality % achieved on a daily basis for last 5 work days, this data is available for one month, say 20 work days.
I have worked out the combinations which is 243. 5 ...
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Reconstruction of Species Distribution based on poorly-sampled data
cross-posted to Signal Processing, World Building, and Biology Stack Exchange
Problem: After reading a series of fantasy novels, I noticed that the biosphere in that world made no sense. To clarify, ...
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What is this "PCA-based re-ordering" for a correlation heatmap / correlogram? [duplicate]
The R function corrgram (in the corrgram package) offers several options for re-ordering the correlation matrix. One of them is ...
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1answer
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Interpretation of this heatmap
Consider a synthetically generated dataset. Assume we have two groups of people, one is given diet pills, the other a placebo. Their weights are measured at 4 different days, namely, ...
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Data Visualization: Alternatives to Choropleth maps for spatial data and statistical graphics
This question is about data visualization and statistical graphics. I have been trying to present statistical data in map. The data is at county level in the US and also at time state level. My data ...
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Data rescaling for a more informative heatmap?
I have a 2000$\times$2000 matrix of values. Over half of the values are 0, and for those non-zeros, most of them are less than 10, but the maximum value is 140.
So when I do a heatmap, it looks like ...
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1answer
339 views
Correlation heatmaps with batch effects
I am interested in plotting correlation heat maps for a multivariate dataset collected in two batches. Some of the variables show a clear batch effect others do not show any batch effect. Is there ...
