STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
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When I run "h5ad2rds.R" to convert .h5ad file to .rds format, get error"Error in UpdateKey(key = layer) : could not find function "UpdateKey"" #261

Closed JJJaneeee closed 4 months ago

JJJaneeee commented 5 months ago

Hey guys! When I run 'h5ad2rds.R' to convert h5ad file to .rds format, I met error"Error in UpdateKey(key = layer) : could not find function "UpdateKey". Maybe "UpdateKey" function is a function in"SeuratDisk", and I have installed the package"SeuratDisk" v0.0.0.9015, It's the latest version, but there is no function"UpdateKey". I want to know how can I use this R script for data conversion?

Thanks for help!

tanliwei-coder commented 5 months ago
name: r-41
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  - r-rocr=1.0_11=r41hc72bb7e_2
  - r-rpart=4.1.19=r41h06615bd_0
  - r-rprojroot=2.0.3=r41hc72bb7e_1
  - r-rspectra=0.16_1=r41h9f5de39_1
  - r-rstudioapi=0.14=r41hc72bb7e_1
  - r-rtsne=0.16=r41h37cf8d7_1
  - r-rvest=1.0.3=r41hc72bb7e_1
  - r-sass=0.4.6=r41ha503ecb_0
  - r-scales=1.2.1=r41hc72bb7e_1
  - r-scattermore=1.1=r41ha503ecb_0
  - r-sctransform=0.3.5=r41h9f5de39_1
  - r-selectr=0.4_2=r41hc72bb7e_2
  - r-seurat=4.3.0=r41h38f115c_0
  - r-seuratobject=4.1.3=r41h38f115c_0
  - r-shape=1.4.6=r41ha770c72_1
  - r-shiny=1.7.4=r41h785f33e_0
  - r-sitmo=2.0.2=r41h7525677_1
  - r-sourcetools=0.1.7_1=r41h38f115c_0
  - r-sp=1.6_1=r41h57805ef_0
  - r-spatial=7.3_16=r41h133d619_0
  - r-spatstat.data=3.0_1=r41hc72bb7e_0
  - r-spatstat.explore=3.2_1=r41h57805ef_0
  - r-spatstat.geom=3.2_1=r41h57805ef_0
  - r-spatstat.random=3.1_5=r41ha503ecb_0
  - r-spatstat.sparse=3.0_1=r41h133d619_0
  - r-spatstat.utils=3.0_3=r41h57805ef_0
  - r-squarem=2021.1=r41hc72bb7e_1
  - r-stringi=1.7.12=r41hc0c3e09_1
  - r-stringr=1.5.0=r41h785f33e_0
  - r-survival=3.5_5=r41h133d619_0
  - r-sys=3.4.2=r41h57805ef_0
  - r-systemfonts=1.0.4=r41h0ff29ef_1
  - r-tensor=1.5=r41hc72bb7e_1004
  - r-textshaping=0.3.6=r41h24cd192_5
  - r-tibble=3.2.1=r41h133d619_1
  - r-tidyr=1.3.0=r41h38f115c_0
  - r-tidyselect=1.2.0=r41hc72bb7e_0
  - r-tidyverse=2.0.0=r41h785f33e_0
  - r-timechange=0.2.0=r41h38f115c_0
  - r-timedate=4022.108=r41hc72bb7e_0
  - r-tinytex=0.45=r41hc72bb7e_0
  - r-triebeard=0.4.1=r41h38f115c_0
  - r-ttr=0.24.3=r41h06615bd_1
  - r-tzdb=0.4.0=r41ha503ecb_0
  - r-urltools=1.7.3=r41h7525677_3
  - r-utf8=1.2.3=r41h133d619_0
  - r-uuid=1.1_0=r41h06615bd_1
  - r-uwot=0.1.14=r41h7525677_1
  - r-vctrs=0.6.2=r41ha503ecb_0
  - r-viridislite=0.4.1=r41hc72bb7e_1
  - r-vroom=1.6.3=r41ha503ecb_0
  - r-withr=2.5.0=r41hc72bb7e_1
  - r-xfun=0.39=r41ha503ecb_0
  - r-xml2=1.3.4=r41h1ad5fc0_1
  - r-xtable=1.8_4=r41hc72bb7e_4
  - r-xts=0.13.1=r41h133d619_0
  - r-yaml=2.3.7=r41h133d619_0
  - r-zoo=1.8_12=r41h133d619_0
  - readline=8.2=h8228510_1
  - referencing=0.32.1=pyhd8ed1ab_0
  - requests=2.31.0=pyhd8ed1ab_0
  - rfc3339-validator=0.1.4=pyhd8ed1ab_0
  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
  - rpds-py=0.17.1=py312h4b3b743_0
  - sed=4.8=he412f7d_0
  - send2trash=1.8.2=pyh41d4057_0
  - setuptools=69.0.3=pyhd8ed1ab_0
  - six=1.16.0=pyh6c4a22f_0
  - sniffio=1.3.0=pyhd8ed1ab_0
  - soupsieve=2.5=pyhd8ed1ab_1
  - stack_data=0.6.2=pyhd8ed1ab_0
  - sysroot_linux-64=2.12=he073ed8_16
  - terminado=0.18.0=pyh0d859eb_0
  - tinycss2=1.2.1=pyhd8ed1ab_0
  - tk=8.6.13=noxft_h4845f30_101
  - tktable=2.10=h0c5db8f_5
  - tomli=2.0.1=pyhd8ed1ab_0
  - tornado=6.3.3=py312h98912ed_1
  - traitlets=5.14.1=pyhd8ed1ab_0
  - types-python-dateutil=2.8.19.20240106=pyhd8ed1ab_0
  - typing-extensions=4.9.0=hd8ed1ab_0
  - typing_extensions=4.9.0=pyha770c72_0
  - typing_utils=0.1.0=pyhd8ed1ab_0
  - tzdata=2023d=h0c530f3_0
  - uri-template=1.3.0=pyhd8ed1ab_0
  - urllib3=2.1.0=pyhd8ed1ab_0
  - wcwidth=0.2.13=pyhd8ed1ab_0
  - webcolors=1.13=pyhd8ed1ab_0
  - webencodings=0.5.1=pyhd8ed1ab_2
  - websocket-client=1.7.0=pyhd8ed1ab_0
  - wheel=0.42.0=pyhd8ed1ab_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.1.1=hd590300_0
  - xorg-libsm=1.2.4=h7391055_0
  - xorg-libx11=1.8.7=h8ee46fc_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.11=hd590300_0
  - xorg-libxt=1.3.0=hd590300_1
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - zeromq=4.3.5=h59595ed_0
  - zipp=3.17.0=pyhd8ed1ab_0
  - zlib=1.2.13=hd590300_5
  - zstd=1.5.5=hfc55251_0
prefix: /data/users/tanliwei/conda/envs/r-41

Here is a conda environment definition, I can run h5ad2rds.R successfully on it, you can copy into a file, like env.yml, and run the command below to create a new conda environment and try again

conda env create -n r-env -f env.yml