DENDRO | Genetic Heterogeneity Profiling by Single Cell RNA | Genomics library
kandi X-RAY | DENDRO Summary
kandi X-RAY | DENDRO Summary
This DENDRO package includes two analysis tools: (1) DENDRO, a phylogenetic tree construction with real dataset such as tumor and hematopoesis scRNA-seq, and (2) DENDROplan, which help design experiment by predicting the accuracy of DENDRO cluster given inferred clonal tree structure, cell number and sequencing depth. Overall pipelines are shown below.
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DENDRO Key Features
DENDRO Examples and Code Snippets
Community Discussions
Trending Discussions on DENDRO
QUESTION
I am using a GUI from QtDesigner to plot Dendrogram. My code is below, but I can not plot the Dendrogram, how can I fix it?
...ANSWER
Answered 2021-Feb-27 at 10:18You have to import the dendrogram from scipy:
QUESTION
I already made a post for this question on biostars forum (https://www.biostars.org/p/452352/) but did not get a lot of replies.
I'm having difficulties to get a plot with a readable scale.
I have plotted transcriptomic data using R with package EMA. However 'genes names' (ordinate axis) are written too big and I can't see all gene names. I would like to have one gene name per compartment.
Here is my code:
...ANSWER
Answered 2020-Aug-03 at 09:51As a workaround you could follow this tutorial by Dave Tang:
QUESTION
I have 72 sample in my datExprSTLMS as gene expression dataset and ran clustering on this data set based on below code:
...ANSWER
Answered 2019-Dec-09 at 13:26Change keepSamples = (Cutreecluster_Sample==!0)
to keepSamples = (Cutreecluster_Sample!=0)
Why? Evaluating your command from right to left: !0
is a logical negation of 0
, which is equivalent to !FALSE
in R. Thus !0
is equal to TRUE
. You then check if Cutreecluster_Sample
equals TRUE
. TRUE
coerced to numeric is 1
in R. Thus your check is actually TRUE
iff samples are in cluster 1, not cluster 0.
Try !0 == 1
and FALSE == 0
.
QUESTION
I have a matrix which has 600 different labels. Therefore, it is really big file; and I couldn't see these labels very well, when I created a figure to cluster my data. How should I create a high resolution file and save it?
I already tried below code.
...ANSWER
Answered 2019-Oct-22 at 14:29The problem is not with your resolution, but the size of the image (or the size of the lines). Since i do not know how to change the linewidth in the dendogram plot, i will just go with the straight forward solution to make a HUGE image.
QUESTION
I've got a heatmap from a FoldChange dataset (176x10) and labeled it using another data.frame (176x2) where I have only the genes (rownames of the main dataset) and their resulting protein abreviation.
Although there are different 176 genes, most of them results in the same protein so I have 22 different abreviations (row labels).
I would like to group the rows by the protein abreviations.
This is the code I'm running, where teste
is the main data.frame and ident
is the identification data.frame:
ANSWER
Answered 2019-Sep-27 at 15:53As mentioned in my comment, you can do this quite easily by ggplot2
facetting. Here's a rough example.
QUESTION
I am trying to apply dendextend in order to color the ggdendro labels. I get this error:
...ANSWER
Answered 2019-Feb-11 at 08:46Seems you were confusing dendrogram with dendrogram data. This will work:
QUESTION
I have a simlarity matrix as follows:
...ANSWER
Answered 2017-Oct-28 at 20:09I have figured it out upon reading one of the examples in R. Here is what one has to do using the similarity matrix.
QUESTION
Hello here is my component :
...ANSWER
Answered 2017-Oct-22 at 12:38From the documentation:
Components have a well-defined lifecycle Each component can implement "lifecycle hooks". These are methods that will be called at certain points in the life of the component. The following hook methods can be implemented:
- $onInit() - Called on each controller after all the controllers on an element have been constructed and had their bindings initialized (and before the pre & post linking functions for the directives on this element). This is a good place to put initialization code for your controller.
- $onChanges(changesObj) - Called whenever one-way bindings are updated. The changesObj is a hash whose keys are the names of the bound properties that have changed, and the values are an object of the form
So you can just use:
QUESTION
I have the following three dimensional array:
...ANSWER
Answered 2017-Oct-17 at 05:09Try this:
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