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Questions - scanpy

scv.pl.proportions(): numpy.AxisError in `Cellrank` workflow

I am new to use python to anlyze scRNA-seq. I run the cellrank workflow and always found this error. Here is my code for Cellrank: import scvelo as scv import scanpy as sc import cellrank import nump...
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jpx

seurat

scanpy

Votes: 0

Answers: 1

Latest Answer

scv.pl.proportions gives the proportion of spliced and unspliced reads in your dataset. These count tables must be added to your adata layers before you can call this function. Your adata object does ...
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badwolf

scanpy correlation matrix with dendrogram

I tried to recreate the correlation matrix that is described in scanpy's tutorial, using my own RNAseq dataset. The relevant function in scanpy is: sc.pl.correlation_matrix and the plot looks like thi...
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Ofir Shorer

python

matrix

pearson-correlation

scanpy

Votes: 0

Answers: 1

Latest Answer

I managed to solve this problem with some trial and error method. Indeed, it is impossible to obtain a single scalar from a correlation between two unequal-sized matrices. In fact, the correlation in ...
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Ofir Shorer

Receiving "TypeError: __init__() got an unexpected keyword argument 'basey'" In this tutorial

I've been trying to run through this tutorial (https://bedapub.github.io/besca/tutorials/scRNAseq_tutorial.html) for the past day and constantly get an error after running this portion: bc.pl.kp_gene...
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SorenFlying

python

python-3.x

rna-seq

scanpy

Votes: 0

Answers: 4

Latest Answer

I had a similar problem when I tried to scale the y-axis of my plot logarithmically. Thereby the base should be 2. I had success when I tried base=2 instead of basey=2. plt.yscale("log",base...
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Chris

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