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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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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2answers
107 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 ...
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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
734 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 ...
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1answer
18 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 (...
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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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107 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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7answers
8k 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 ...
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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
200 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
427 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
180 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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1answer
277 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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278 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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1answer
354 views
Does heights betwen 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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775 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 ...
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310 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 ...
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580 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 ...
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1answer
993 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 ...
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105 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 ...
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0answers
46 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) ...
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42 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, ...
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1answer
774 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 ...
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1answer
71 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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334 views
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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2answers
232 views
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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0answers
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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
2k views
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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2answers
3k views
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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1answer
486 views
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
255 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 ...
