Closed julierodor closed 5 years ago
scottgigante
commented
5 years ago Hi @julierodor , thanks for the error report. I've made a change which should hopefully fix your problem. If you're willing to install from github to check for me before I push the fix to CRAN, I'd appreciate it.
devtools::install_github("KrishnaswamyLab/phateR", ref="dev")
julierodor
commented
5 years ago Hi, I tried the command you suggested. The installation seems to work (see below - #Installation). But I still have errors when running phateR through RunPHATE command (see below # running phate with RunPHATE) Phate_Cluster6 <- RunPHATE(Phate_Cluster6,genes.use = Phate_Cluster6@var.genes,max.dim = 2,reduction.name = "phate2d")
✔ checking for file ‘/tmp/RtmpfkBhI9/remotes1be74f68ac60/KrishnaswamyLab-phateR-ed36e16/DESCRIPTION’ ... ─ preparing ‘phateR’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘phateR_0.4.0.9999.tar.gz’
Installing package into ‘/home/jrodor/R/x86_64-pc-linux-gnu-library/3.5’ (as ‘lib’ is unspecified)
Error in py_module_import(module, convert = convert) : AttributeError: module 'pandas' has no attribute 'core'
Detailed traceback:
File "/home/jrodor/.local/lib/python3.6/site-packages/phate/init.py", line 5, in
Argument k is deprecated. Using knn instead. Argument alpha is deprecated. Using decay instead. Argument use.alpha is deprecated. Alpha-decay is on by default. Error loading Python module phate AttributeError: module 'pandas' has no attribute 'core'
Detailed traceback:
File "/home/jrodor/.local/lib/python3.6/site-packages/phate/init.py", line 5, in
scottgigante
commented
5 years ago Hi @julierodor , thanks for the detailed traceback. Looks like the issue with phateR is resolved, but your python environment has a separate issue. Could you please run the following from a terminal?
pip uninstall pandas
pip uninstall phate
pip install --user phateand then try again?
julierodor
commented
5 years ago Hi, Thanks. It seems to work now (see below). I am guessing the messages about the argument deprecated refer to the update. Is that correct? I am trying to reproduce data from someone else. I have the script but not sure which version of phate they have been using. I will check if the downstream analysis differs from the previous results but which differences should I expect between this version and the previous ones? Julie
Argument k is deprecated. Using knn instead. Argument alpha is deprecated. Using decay instead. Argument use.alpha is deprecated. Alpha-decay is on by default. Calculating PHATE... Running PHATE on 3962 cells and 1446 genes. Calculating graph and diffusion operator... Calculating PCA... Calculated PCA in 12.98 seconds. Calculating KNN search... Calculated KNN search in 1.80 seconds. Calculating affinities... Calculated affinities in 1.50 seconds. Calculated graph and diffusion operator in 16.31 seconds. Calculating landmark operator... Calculating SVD... Calculated SVD in 4.09 seconds. Calculating KMeans... Calculated KMeans in 82.60 seconds. Calculated landmark operator in 88.02 seconds. Calculating optimal t... Automatically selected t = 10 Calculated optimal t in 19.66 seconds. Calculating diffusion potential... Calculated diffusion potential in 21.06 seconds. Calculating metric MDS... Calculated metric MDS in 21.99 seconds. Calculated PHATE in 167.04 seconds.
scottgigante
commented
5 years ago Great! Yes, the deprecation arguments are due to the update - no change in functionality there, just some argument names have changed. Glad to hear it's working!
Hi, I have been using phateR through Seurat command RunPHATE. I have been successful before but now the same command gives me some error (see below). I am not sure if it's due to some updates and how to fix it. Any help would be appreciated. Thanks The command I am using is RunPHATE(Phate_Cluster6,genes.use = Phate_Cluster6@var.genes,max.dim = 2,reduction.name = "phate2d")
error Argument k is deprecated. Using knn instead. Argument alpha is deprecated. Using decay instead. Calculating PHATE... Running PHATE on 3962 cells and 1446 genes. Calculating graph and diffusion operator... Calculating PCA... Calculated PCA in 13.30 seconds. Calculating KNN search... Calculated KNN search in 1.84 seconds. Calculating affinities... Calculated affinities in 1.47 seconds. Error in py_call_impl(callable, dots$args, dots$keywords) : TypeError: init() got an unexpected keyword argument 'use.alpha'
Detailed traceback: File "/home/jrodor/.local/lib/python3.6/site-packages/phate/phate.py", line 808, in fit_transform self.fit(X) File "/home/jrodor/.local/lib/python3.6/site-packages/phate/phate.py", line 715, in fit (self.kwargs)) File "/home/jrodor/.local/lib/python3.6/site-packages/graphtools/api.py", line 248, in Graph return Graph(params) File "/home/jrodor/.local/lib/python3.6/site-packages/graphtools/graphs.py", line 102, in init super().init(data, n_pca=n_pca, kwargs) File "/home/jrodor/.local/lib/python3.6/site-packages/graphtools/graphs.py", line 473, in init super().init(data, kwargs) File "/home/jrodor/.local/lib/python3.6/site-packages/graphtools/base.py", line 750, in init super().init(data, kwargs) File "/home/jrodor/.local/lib/python3.6/site-packages/graphtools/base.py", line 135, in init super().init(kwa