Exploring dimension-reduced embeddings

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Text Data & NLP sleepwalk
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sleepwalk

Exploring dimension-reduced embeddings

This is the code repository. See here for the Sleepwalk web page.

License and disclaimer

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Comments
  • Error running sleepwalk: cannot open the connection

    Error running sleepwalk: cannot open the connection

    Dear sleepwalk developers, Thanks a lot for providing such nice method. I could install the package but I get the following error when I tried to run:

    > sleepwalk(myseuratobj@[email protected], myseuratobj@[email protected])
Estimating 'maxdist' for feature matrix 1
Server has been stopped.
Server has been stopped.
Error in app$openPage(useViewer, browser) : 
  Timeout waiting for websocket.
In addition: Warning messages:
1: In file(con, "r") :
  cannot open file 'sleepwalk_canvas.html': No such file or directory
2: In func(req) : File '/favicon.ico' is not found

    I know this is probably not a sleepwalk specific error, but I couldn't find a solution for this. Any hints/help on how to fix this issue?

    Also, I have a question about the output. Besides using the interactive mode to manually inspect cells that might be "misplaced" on the reduced-dimension space, I would like to systematically find the cells that don't quite fit to the clusters they were originally assigned to. In other words, how would you suggest to use sleepwalk to refine my clustering since I suspect that many of my cells were wrongly assigned to their clusters. I am using Seurat package to reduce dimension and clustering.

    Thank you very much, Gustavo

    opened by gufranca 2
  • Error: 'browser' must be a non-empty character string

    Error: 'browser' must be a non-empty character string

    Hello,

    After calling the sleepwalk function on a Seurat object, I got this error:

    > sleepwalk( as.matrix(BAM@[email protected]), as.matrix(BAM@[email protected]) )

Estimating 'maxdist' for feature matrix 1
Error in browseURL(str_c("http://localhost:", port, "/", pageobj$startPage),  :
  'browser' must be a non-empty character string

    I have loaded the stringr library (containing the function str_c()), and I cannot find the file originating this error. Can I ask if someone had this problem at some point?

    Thank you

    opened by PedroRaposo 2
  • slw_on_selection error when sleepwalk is not attached

    slw_on_selection error when sleepwalk is not attached

    Running sleepwalk without attaching the package (i.e., NOT specifying library(sleepwalk)) like this works fine:

    sleepwalk::sleepwalk(seurat@[email protected], t(seurat@data[[email protected],]))

    But the moment you select cells with your mouse, it crashed (browser tab closes) and R gives this error:

    Error in slw_on_selection(selPoints, 1) : could not find function "slw_on_selection"

    Loading the package using library(sleepwalk) solves the issue, but it'd be nice if it weren't necessary.

    opened by FelixTheStudent 0
  • doc for comparison

    doc for comparison

    The example on the web page for comparing two embeddings still uses the old version where both distances are used concurrently. We also need to change the explanation below to say that the same cell always has the same colour in all embeddings

    opened by simon-anders 0
  • Suggestion: Link embeddings from transposed table

    Suggestion: Link embeddings from transposed table

    Let say I have e.g. a matrix where I have individuals (cells e.g.) as rows and features as columns, and then run a UMAP on both the ordinary matrix, and the transposed one. Then it would be natural to want to look at the individual UMAP with the default usage (the distances to other individuals), but it would also be interesting to see the features for that individual (and vice versa).

    Is it clear what I mean?

    opened by StaffanBetner 2
Releases(v0.3.2)

  • v0.3.2(Sep 17, 2021)

    • jrc now (v.0.5.0) uses setLimits function for all the security restriction. This update fixes the dependency problem caused by that change.
    Source code(tar.gz)
    Source code(zip)

  • v0.3.1(Sep 30, 2020)

  • v.0.3.0(Feb 27, 2020)

    • New argument metric allows to use angular distance (metric = "cosine") as an alternative to default Euclidean distance (meric = "euclid").

    • If compare = "distances", it is no longer required to provide several embeddings. If only one embedding is given, it will be used for all the distances.

    Source code(tar.gz)
    Source code(zip)

  • v0.2.1(Oct 2, 2019)

    • Changes due to an update of the jrc package.

    • Indices of selected points are no longer stored in a variable and can be accessed only via the callback function. Thus, no changes to the global environment are made, unless user specifies them his- or herself.

    • Added the possibility to pass arguments to jrc::openPage (such as port number or browser in which to open the app.)

    Source code(tar.gz)
    Source code(zip)

  • v0.2.0(Sep 27, 2019)

    • Now HTML Canvas is used to plot the embedding. It makes Sleepwalk faster and allows to simultaneously display more points.

    • New parameter mode = c("canvas", "svg") is added, that allows user to go back to the old SVG-based version of Sleepwalk app.

    • Bug in slw_snapshot is fixed. The function no longer returns a list of identical plots, when used with several different embeddings.

    Source code(tar.gz)
    Source code(zip)
Owner
S. Anders's research group at ZMBH
S. Anders's research group at ZMBH
GitHub https://anders-biostat.github.io/sleepwalk/
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