azimuth | A Shiny web app for mapping datasets using Seurat v4 | Genomics library

 by   satijalab R Version: v0.4.6 License: GPL-3.0

kandi X-RAY | azimuth Summary

kandi X-RAY | azimuth Summary

azimuth is a R library typically used in Artificial Intelligence, Genomics applications. azimuth has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Azimuth is a Shiny app demonstrating a query-reference mapping algorithm for single-cell data. The reference data accompanying the app and the algorithms used are described in the publication “Integrated analysis of multimodal single-cell data” (Y. Hao, S. Hao, et al., Cell 2021).

            kandi-support Support

              azimuth has a low active ecosystem.
              It has 71 star(s) with 14 fork(s). There are 8 watchers for this library.
              It had no major release in the last 6 months.
              There are 27 open issues and 66 have been closed. On average issues are closed in 36 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of azimuth is v0.4.6

            kandi-Quality Quality

              azimuth has 0 bugs and 0 code smells.

            kandi-Security Security

              azimuth has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              azimuth code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              azimuth is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              azimuth releases are not available. You will need to build from source code and install.
              Installation instructions, examples and code snippets are available.

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            azimuth Key Features

            No Key Features are available at this moment for azimuth.

            azimuth Examples and Code Snippets

            No Code Snippets are available at this moment for azimuth.

            Community Discussions


            Python plot signals based on the azimuth of arrival?
            Asked 2022-Apr-04 at 17:52

            I'm trying to make a plot of a signal, where the orientation of the signal on the plot is the azimuth the signal originated from.

            My initial thought was to use a polar projection, but I don't actually want the signal itself to be converted into polar coordinates.

            I tried to remedy the polar conversion by using a polar projected image as a background to a subplot grid, rotating the subplots based on the azimuth, similar to what's found in this link: Rotate transformation on matplotlib axis in subplot

            Here's the plot that I created using matplotlib following this workflow, showing signals of azimuths 45 degrees apart.

            This plot is kinda what I want, but not exactly. It plots the signals by their azimuth, and still preserves their amplitude and frequency without an actual polar conversion. However, this approach is incredibly hackish and not scalable -- it would be very difficult to insert a signal at 30 degrees, for example, and the signals at 135 & 225 degrees don't show up at all.

            I think my problem is that I'm conceptualizing the problem incorrectly. I've tagged PyGMT here because I know there is a way to create the plot I want using it, but finding a springboard example with that library has proved difficult for me. Any insights are greatly appreciated.



            Answered 2022-Apr-04 at 17:52

            In the office chance anyone ever needs something similar, here's what I was able to cobble together. I used PyGMT to create the figure I needed -- if you're not already familiar with Generic Mapping Tools (GMT) syntax, it can be difficult to learn. Below is the script I created to generate a random sequence of signals of various amplitudes and frequencies with corresponding "azimuths" that simulate their propagation direction or arrival direction.




            How to combine two polar charts?
            Asked 2022-Mar-29 at 17:28

            I founded a very interesting code that allows to combine two differents charts.

            I would like to do the same with two polar charts to permit multiple scale, but there is no renderer as line and shape or bar. Is there nevertheless a way to do that ?

            The aim is to plot to series with big dynamic difference like distance & site of laser shoots for each azimuth, something like that:




            Answered 2022-Mar-29 at 17:28

            While I'm not aware of any support for nesting multiple polar plots with differing scales, jfreechart does support zooming, as described here. Absent a domain axis, zooming is limited to the range axis. Because the zooming controls may be counterintuitive in this context, the variation below adds plot-specific controls: The getZoomOutAction() simply invokes the chart panel's restoreAutoBounds() method, like this, while the getZoomInAction() extends the range by 50%, like this.



            Radially 'sweep out' a 2D contour plot to create a 3D plot (Python, Matplotlib)
            Asked 2022-Mar-27 at 02:33

            I have three 1D arrays, which represent radius, height, and an intensity measured at that point. I have plotted these to create a 2D contour map. A simple example of the way in which the data is stored is below:



            Answered 2022-Mar-27 at 02:33

            Technically you cannot rotate a 2D plot and get a 3D surface. You can only rotate a 2D curve and get a 3D surface. If this is the case, you could do it as:



            Running nested user-defined function in `terra::app()` on multiple cores
            Asked 2022-Mar-24 at 20:38

            PREFACE My error is a simple "Mathematical operation applied to non-numeric argument" error, but I think this arise from how I create a suite of user defined functions and use them within the terra::app() function. I am going to describe the full workflow to elucidate what I am after, so please bare with me.

            ISSUE I am trying to apply a statistical-empirical topographic correction to Sentinel 2A data in R. To apply the topographic correction, I have appended rasters of solar azimuth, solar zenith, and slope and aspect to the multiband scene. I am first taking a random sample of each band within a scene to get its intensity value as well as the corresponding solar zenith, aspect, and slope values. From there, I calculate the cosine of the solar incident angle for each sampled cell using the zenith, azimuth, slope and aspect using a user-define function. Then, I run a linear regression between the cosine of solar incident angle and the respective intensity value for each band. I then apply a user-defined function that calls the solar incident function above using the terra::app() function to finalize the topographic information from these linear regressions. This works on one core just fine with fake data, but is painfully slow with real Sentinel data, so I want it to work on multiple cores. When I try to run on multiple cores I get the error:



            Answered 2022-Mar-24 at 20:38

            It dawned on me after a good night's sleep that the answer might have been much simpler than I realized. I just needed to run the cos_i() function using terra::app(), but everything else would work fine and quickly using standard raster algebra provided by the terra:: package. Therefore, I could eliminate the RAST_CORR() function and make the extra steps basic raster algebra.



            Struggling to get attributes from XML (PHP)
            Asked 2022-Mar-22 at 16:36

            I have the following XML returned by an API:



            Answered 2022-Mar-22 at 16:36

            There is one problem with this XML sample: it contains a HTML entity ° that is not a valid XML entity. The contents of should probably be wrapped in a CDATA object.

            If you fix that, you can register the ns3 namespace and use XPath to get to the entities:



            Reading and plotting HDF5(.h5) file and showing map for a specific latitude and longitude
            Asked 2022-Mar-18 at 16:11

            I got a HDF5 file from MOSDAC website named 3DIMG_30MAR2018_0000_L1B_STD.h5 and I'm tying to read the this file and visualize the TIR and VIS dataset in the file in map. Since I am new to programming I don't have much idea how to do this for a specific location on the global data using the Latitude and longitude values. My problem statement is to show data for Indian region.

            The coding I have done till now:



            Answered 2022-Mar-08 at 18:38

            Updated 2022-03-08: Pseudo-code in my original post used plt.contourf() to plot the data. That does not work with raster image data saved in 'IMG_TIR1' dataset. Instead, plt.imshow() must be used. See detailed answer posted on 2022-03-07 for the complete procedure.

            All 'IMG_name' datasets are raster image data. I modified the code to show a simple example that reads the HDF5 file with h5py, then plots the image data with matplotlib and cartopy on a Geostationary (original satellite) projection. I picked cartopy based on this comment on the Basemap site: "Deprecation Notice: Basemap is deprecated in favor of the Cartopy project." I'm sure it can be modified to use Basemap to plot and NetCDF to read the HDF5 file.

            Updated code below:



            Animating distantLight filter with svg.js
            Asked 2022-Mar-11 at 09:33

            I am attempting to create a simple SVG animation using SVG.js. My desired result would be equivalent to:



            Answered 2022-Mar-11 at 09:33

            According to this comment there is actually a constructor for a distantLight (and other types of light) filter inside the diffuseLight filter class. When initialised via those constructors distantLight filter does support animations properly. All credit for this answer goes to Fuzzyma.



            SketchUp Ruby - Display a message box to user if they clicked on a line in SketchUp
            Asked 2022-Mar-09 at 08:47

            I am trying to develop a custom tool which will allow the user to select a line and they will be given the slope distance, azimuth and zenith angle of the line. A small table with all that info will then appear on their screen.

            I currently have a little bit of code written which you can see below:



            Answered 2022-Mar-09 at 08:47

            The code below might help you with creating class variables of the selected edge's vertex start & end positions of X, Y, Z coordinates. These values might be needed to calculate some math formulas. Let me know if it helped or not.

            I recommend encapsulating your code with Ruby modules for variable or method names not clashing with other SketchUp scripts on the Plugins folder.



            MediaPipe hands-detection hands.process waits forever
            Asked 2022-Mar-07 at 13:53

            When I run the following Python file



            Answered 2022-Mar-07 at 13:53

            I think there is something wrong with tensorflow in my mac installation.

            I now run it with Docker so I don't have the environment problem.

            I have the following Dockerfile



            How to change background and outline color on topographic map?
            Asked 2022-Feb-28 at 00:14

            I followed this excellent guide by Adam Symington and successfully created the following topographic map of Sabah (a state in Malaysia, which is a Southeast Asian nation). The awkward blob of black in the upper left corner is my attempt to plot certain coordinates on the map.

            I would like to improve this diagram in the following ways:

            EDIT: I have figured item (1) out and posted the solution below. (2) and (3) pending.

            1. [SOLVED] The sch dataframe contains coordinates of all schools in the state. I would like to plot these on the map. I suspect that it is currently going wonky because the axes are not "geo-axes" (meaning, not using lat/lon scales) - you can confirm this by setting ax.axis('on'). How do I get around this? [SOLVED]

            2. I'd like to set the portion outside the actual territory to white. Calling ax.set_facecolor('white') isn't working. I know that the specific thing setting it to grey is the ax.imshow(hillshade, cmap='Greys', alpha=0.3) line (because changing the cmap changes the background); I just don't know how to alter it while keeping the color within the map as grey.

            3. If possible, I'd like the outline of the map to be black, but this is just pedantic.

            All code to reproduce the diagram above is below. The downloadSrc function gets and saves the dependencies (a 5.7MB binary file containing the topographic data and a 0.05MB csv containing the coordinates of points to plot) in a local folder; you need only run that once.



            Answered 2022-Feb-28 at 00:14

            As it turns out, I had given myself the hint to answering point (1), and also managed to solve (2).

            For (1), the points simply needed to be rescaled, and we get this:

            I did so by getting the max/min points of the map from the underlying shapefile, and then scaling it based on the max/min points of the axes, as follows:


            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

            Install azimuth

            Note: you may need to update some packages prior to installing Azimuth; from a fresh R session run:.


            We do not actively support users running the app themselves and suggest you use version 4 of the Seurat package to run the reference mapping workflow and related visualizations on your local system. Please see the Seurat mapping vignette for an example of how to use Seurat for reference mapping. If you use the instance of the app we are hosting on the web, you can download a Seurat v4 R script once your analysis is complete that will guide you in reproducing the analysis. You do not need Azimuth to reproduce the analysis. If you would like to help us improve the app, and you believe a dataset meets the requirements and it is publicly available for us to use for debugging but the app doesn’t work, please file a Github issue linking to the dataset and describing the problem on the issues page.
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