search

maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
104 stars 40 forks source link

cbImportSeurat2 not working on an rds file? #106

Closed matthewspeir closed 5 years ago

matthewspeir commented 5 years ago

Not really sure what's going on, but calling cbImportSeurat2 on the rds file results in the following errors:

Loading required package: Seurat
Loading required package: ggplot2
Loading required package: cowplot

Attaching package: ‘cowplot’

The following object is masked from ‘package:ggplot2’:

    ggsave

Loading required package: Matrix
Reading ../chimera-tal1/corrected_pcas.rds
Exporting Seurat data to ./cbImportSeurat_chimera_tal1
Seurat Version installed: 2.3.4
Error in message("Object was created with Seurat version ", object@version) :
  trying to get slot "version" from an object of a basic class ("list") with no slots
Calls: ExportToCellbrowser -> message
Execution halted

Command: 

cbImportSeurat2 -i ../chimera-tal1/corrected_pcas.rds -o ./cbImportSeurat_chimera_tal1

Data location:

Input: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/chimera-tal1
Output: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/mouseGastrulationChimeraTal1/cbImportSeurat_chimera_tal1
maximilianh commented 5 years ago

Most likely this object wasn’t from Seurat or is in an unusual format. I’ll look into it tomorrow.

On Wed 1 May 2019 at 22:50, Matt Speir notifications@github.com wrote:

Not really sure what's going on, but calling cbImportSeurat2 on the rds file results in the following errors:

Loading required package: Seurat

Loading required package: ggplot2

Loading required package: cowplot

Attaching package: ‘cowplot’

The following object is masked from ‘package:ggplot2’:

ggsave

Loading required package: Matrix

Reading ../chimera-tal1/corrected_pcas.rds

Exporting Seurat data to ./cbImportSeurat_chimera_tal1

Seurat Version installed: 2.3.4

Error in message("Object was created with Seurat version ", object@version) :

trying to get slot "version" from an object of a basic class ("list") with no slots

Calls: ExportToCellbrowser -> message

Execution halted

Command:

cbImportSeurat2 -i ../chimera-tal1/corrected_pcas.rds -o ./cbImportSeurat_chimera_tal1

Data location:

Input: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/chimera-tal1

Output: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/mouseGastrulationChimeraTal1/cbImportSeurat_chimera_tal1

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/106, or mute the thread https://github.com/notifications/unsubscribe-auth/AACL4TNKWREMTL2HVVMRSBLPTH7ADANCNFSM4HJX5ZAA .

maximilianh commented 5 years ago

This is not a Seurat object. It just contains a table with PC coordinates. To convert it, you'll have to run R and do this:

d = readRDS("corrected_pcas.rds") write.table(d, "pcaCoords.tsv", sep="\t")

You'll probably have to fix the headers manually and massage the file a bit with cut to get it into a reasonable format.

I'll check if I can easily catch this error in the converter.

On Wed, May 1, 2019 at 11:29 PM Maximilian Haeussler maximilianh@gmail.com wrote:

Most likely this object wasn’t from Seurat or is in an unusual format. I’ll look into it tomorrow.

On Wed 1 May 2019 at 22:50, Matt Speir notifications@github.com wrote:

Not really sure what's going on, but calling cbImportSeurat2 on the rds file results in the following errors:

Loading required package: Seurat

Loading required package: ggplot2

Loading required package: cowplot

Attaching package: ‘cowplot’

The following object is masked from ‘package:ggplot2’:

ggsave

Loading required package: Matrix

Reading ../chimera-tal1/corrected_pcas.rds

Exporting Seurat data to ./cbImportSeurat_chimera_tal1

Seurat Version installed: 2.3.4

Error in message("Object was created with Seurat version ", object@version) :

trying to get slot "version" from an object of a basic class ("list") with no slots

Calls: ExportToCellbrowser -> message

Execution halted

Command:

cbImportSeurat2 -i ../chimera-tal1/corrected_pcas.rds -o ./cbImportSeurat_chimera_tal1

Data location:

Input: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/chimera-tal1

Output: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/mouseGastrulationChimeraTal1/cbImportSeurat_chimera_tal1

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

maximilianh commented 5 years ago

Wow, that was easy. the same command now shows:

Loading required package: Matrix Reading ../chimera-tal1/corrected_pcas.rds Error: The input .rds file does not seem to contain a Seurat object Execution halted

On Thu, May 2, 2019 at 4:06 PM Maximilian Haeussler maximilianh@gmail.com wrote:

This is not a Seurat object. It just contains a table with PC coordinates. To convert it, you'll have to run R and do this:

d = readRDS("corrected_pcas.rds") write.table(d, "pcaCoords.tsv", sep="\t")

You'll probably have to fix the headers manually and massage the file a bit with cut to get it into a reasonable format.

I'll check if I can easily catch this error in the converter.

On Wed, May 1, 2019 at 11:29 PM Maximilian Haeussler maximilianh@gmail.com wrote:

Most likely this object wasn’t from Seurat or is in an unusual format. I’ll look into it tomorrow.

On Wed 1 May 2019 at 22:50, Matt Speir notifications@github.com wrote:

Not really sure what's going on, but calling cbImportSeurat2 on the rds file results in the following errors:

Loading required package: Seurat

Loading required package: ggplot2

Loading required package: cowplot

Attaching package: ‘cowplot’

The following object is masked from ‘package:ggplot2’:

ggsave

Loading required package: Matrix

Reading ../chimera-tal1/corrected_pcas.rds

Exporting Seurat data to ./cbImportSeurat_chimera_tal1

Seurat Version installed: 2.3.4

Error in message("Object was created with Seurat version ", object@version) :

trying to get slot "version" from an object of a basic class ("list") with no slots

Calls: ExportToCellbrowser -> message

Execution halted

Command:

cbImportSeurat2 -i ../chimera-tal1/corrected_pcas.rds -o ./cbImportSeurat_chimera_tal1

Data location:

Input: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/chimera-tal1

Output: /hive/users/mspeir/cellbrowserTest/mouse_gastrulation/mouseGastrulationChimeraTal1/cbImportSeurat_chimera_tal1

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

matthewspeir commented 5 years ago

Thanks for the commands, Max. I'll give those a shot.