HeatMap | Heat map generation tools
kandi X-RAY | HeatMap Summary
kandi X-RAY | HeatMap Summary
This is a quick program to generate heat maps from trace files. I wrote it in 3 hours, so it’s probably buggy (especially input checking).
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QUESTION
I am a fairly new Python user and have been using pandas and matplotlib to do some data analysis for my research. In particular, I have a data file with 3 sets of data inside: 2 column vectors and an array (see link here to google drive for a simple 3x3 sample of the same format:Sample data. In the end, I need to plot this as a 2D heatmap with the column vectors specifying x and y axis and the array filling my heat points.
I could use pandas.read_csv() with skiprows to do this for one file, but the dimension of each vector and array varies across all of the simulations I have run. Thus, I would have to find the start and end of each set of data for each different file. The biggest files I have are (229, 1), (229, 1), (229, 229).
My question is this: is there a way to specify a start and end to each set of data based on the formatting approach that my output files have? This could be done either into pandas dataframe or into arrays. I prefer dataframes only for the ease of performing computations before plotting.
Any help would be much appreciated!
...ANSWER
Answered 2021-Jun-12 at 03:01There are a lot of ways to do this, I think it's all about data preprocessing or cleaning.
Here's some tips:
- your 3 datasets in 1 file are split by '\n\n' (two continual \n), you can
open()
it, then.read()
all content, then.split('\n\n')
it first. - for each split dataset, the first row is not important(or just has some name or (row,column) info), if they have some sort rule, you could simply skip it (maybe
.split('\n')[1:]
). - for each split dataset, other rows is the data content, you can pass it to
pd._read_csv
or something like that.
Hope these tips can help you.
QUESTION
I need to render a heatmap with 5000x5000 size (25 million points) and update it every 10 seconds.
Question: What approach I should follow if I would like to write this from scratch?
...ANSWER
Answered 2021-Jun-11 at 09:39If you are displaying this in a single regular monitor (Full HD) that has a 1920 x 1080 resolution you won't probably be able to display every single point.
This is because the resolution is actually the number of pixels you can represent - so your max, considering you are using the whole screen, would be 1920 pixels x 1080 pixels (~2M pixels/dots).
So, in order to represent the amount of pixels you want, in a single regular monitor you have to go with the options below:
- Group the items;
- Adding a panel with scrolling bars;
- Reduce the data set.
After you decide on your strategy, you can use the D3 javascript library to plot it.
Here you can find a good post about a strategy to group the items and them plot them using D3: https://int21.io/post/50-million-points/index.html
QUESTION
Is there a fundamental minimum height for a highcharts heatmap?
What we're trying to achieve is a very wide heatmap, that is 1 cell tall and 4,032 to 4,462 cells wide, with the chart pushed out the edge of the frame.
Charts options are currently:
...ANSWER
Answered 2021-Jun-11 at 09:25Here: http://jsfiddle.net/BlackLabel/e9Lp3xvu/ I have reproduced the issue without Angular.
The problem is caused by the default value of tickPixelInterval
for y-axis (72). As a solution you can reduce the value.
QUESTION
In a heatmap, how could I create a three-color gradient, with blue for negative values, red for positive values and white for zero, such that with many zero values, much of the heatmap would be white (and not light red as with the default gradient).
...ANSWER
Answered 2021-Jun-10 at 22:07You can compute the maximum absolute value in your array, then use it to set the clims
argument. c.f. http://docs.juliaplots.org/latest/generated/attributes_subplot/
QUESTION
In Vaadin 14.6.1, I tried to create a Vaadin heatmap foollowing the documentation / example from here.
However, I encountered a few problems/questions, listed in descending order of importance below:
- The heatmap supported 30 rows by 30 columns; but when I tried 40 rows by 40 columns, the entire heatmap showed a single color (blue in my case).
- Is it possible to manually set the minimum numeric value and maximum numeric value for the color scheme. This way, if I plot my data one day and it has values in the range of 0 to 1, but on another dataset from another day, the numeric values range from between 0 and 0.5, the color scheme range won't automatically change (to being between 0 and 0.5) and confuse the user.
- In the documentation, it has the following methods listed, but they do not seem to exist in Vaadin 14.6.1
ANSWER
Answered 2021-May-27 at 15:02I'm not that experienced with Vaadin Chart, but these are the questions that I can comment on:
(1) With 40x40 items you go over the threshold of 1000 in which the Chart switches into "turbo" mode for performance reasons. This seems to not be compatible with the heatmap series. You can disable turbo mode by setting plotOptions.setTurboThreshold(0);
(2) Unfortunately the ColorAxis
doesn't support this, it only has an API for min and max color. Definitely a valid use-case though, and it seems to be supported by the Highcharts library that the Vaadin Chart uses under the hood. You should consider opening a feature request for this in the Github repo.
(3) This seems to be a documentation issue. The methods are available in later Vaadin platform versions, but not in 14.6.
(5) In theory not, but in practice there will be a huge performance hit in the browser due to the excessive amount of DOM elements (quick test of 100x100 froze the browser for 10s). I'm afraid the component isn't really made for such extreme use-cases. In this case it might be better to utilize a low-level JS drawing library using the canvas, or draw an image on the server-side and display that in the browser. Maybe you can also consider modifying your use-case so that you only display one slice of your data and allow the user to switch between slices.
QUESTION
How can I mask the lower triangle while hierarchical clustering with seaborn's clustermap?
...ANSWER
Answered 2021-Jun-09 at 21:34Well, the clustermap
clusters the values according to similarity. This changes the order of the rows and the columns.
You could create a regular clustermap, and in a second step apply the mask:
QUESTION
I am using hv.HeatMap
to plot a connectiviy matrix. I would like to disable the viszualization of the gridlines. At first I thought this should be possible be disabling show_grid
but this does not have any effect on the gridlines.
For example, how would one disable the visulization in the last example from the documentation?
...ANSWER
Answered 2021-Jun-09 at 14:02To activate or deactivate a grid you can add show_grid=True
or show_grid=False
to opts.HeatMap(...)
.
But in your example there is no grid activated, so you can't deactivate the grid lines. The white lines you can see are coming through the background color (which is defined by default as white).
You could change the background adding bgcolor ='#ABABAB'
to opts.HeatMap(...)
, which makes a figure like
But sometimes you have to apply the changes you want to make directly in the bokeh figure object because not all the possibilities are added to holoviews
keyword arguments. If you have to do this, you can follow this introduction.
Extend your example with the following to add an alpha value to the background as an example:
QUESTION
I want to create a nice graph in python, so I used plotly to create a graph, but I get an error.
Maybe because I'm new to plotly
, I don't understand the error in this code.
The only thing I can tell is that my code is wrong.
I want to display multiple graphs in plotly.
ANSWER
Answered 2021-Jun-07 at 03:56According to the documentation on adding traces to subplots, the add_trace
and append_trace
methods only take accept plotly graph_objects
. Therefore, your code block:
QUESTION
I am working on a dataset
...ANSWER
Answered 2021-Jun-04 at 21:25Just fill the titles_count
with 1 first, since they denote 1 count per row.
QUESTION
I am creating a heatmap in ggplot2, and I want to reorder the Y-axis.
After looking through past posts I understand how to reorder based on the X- and Y-axes variables, but I want to reorder the Y-axis based on a third, non-plotted, non-numeric variable in my data frame.
My heatmap shows Terms vs Treatments, but each Term has a source database - this is what I want to order the Terms on. As you can see Terms A and D are from database 2, Term B is from database 1, Term C from database 3. So the y-axis should be ordered Term B, Term A, Term D, Term C. It is currently ordered Term D, C, B, A
Edit: This is actually just an extract of my data, I have a lot of terms so would prefer not to have to manually specify the order. I don't have too many databases though, so would be happy to order those manually.
...ANSWER
Answered 2021-Jun-02 at 12:11A quick solution is to add scale_y_discrete and with the limits argument, you can order your y axis with your source variable:
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