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JinmiaoChenLab / cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline
http://jinmiaochenlab.github.io/cytofkit/
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Cell Percentages #28

Open myles5000 opened 6 years ago

myles5000 commented 6 years ago

I'm having trouble viewing the Cell Percentage Heatmap. On every one of over 30 data files, I get the error "dim(X) must have a positive length". I am processing the files using cytofkit_GUI, my transformation method is "cytofAsinh", the cluster method is Rphenograph, and my visualization method is tsne.

I would also like to know how to view exact percentages for each group in the Cell Percentage Line Chart.

MattMyint commented 6 years ago

Hi, I'm able to reproduce this error by loading a cytofkit .Rdata file that holds the merged results of 13 fcs files (i.e. 13 samples). The error occurs when I select only one sample.

Basically, the heatmap generation step returns an error when trying to create a heatmap with just one column. Are each of your 30 data files created by analysing a single fcs file for each one?

The exact percentages can be viewed in the cytofkit output files. There will be a csv generated called "cytofkit__cluster_cell_percentage.csv" (e.g. cytofkit_Rphenograph_cluster_cell_percentage.csv)

myles5000 commented 6 years ago

My files are all created with a single fcs file. I was unaware of the cell percentage csv file though; that should give me the information I need.

On Tue, Mar 13, 2018 at 12:44 AM, MattMyint notifications@github.com wrote:

Hi, I'm able to reproduce this error by loading a cytofkit .Rdata file that holds the merged results of 13 fcs files (i.e. 13 samples). The error occurs when I select only one sample.

Basically, the heatmap generation step returns an error when trying to create a heatmap with just one column. Are each of your 30 data files created by analysing a single fcs file for each one?

The exact percentages can be viewed in the cytofkit output files. There will be a csv generated called "cytofkit__cluster_cell_percentage.csv" (e.g. cytofkit_Rphenograph_cluster_cell_percentage.csv)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/JinmiaoChenLab/cytofkit/issues/28#issuecomment-372553731, or mute the thread https://github.com/notifications/unsubscribe-auth/AarTZV8qaPG7xKOADd4oiyB8lI4eHNPxks5td1yugaJpZM4SctYi .

-- Emeka Fountain

myles5000 commented 6 years ago

I'd meant to include this in the previous email, sorry: is there a way to generate that csv file for data files that use a single fcs file?

On Tue, Mar 13, 2018 at 9:34 AM, Emeka Fountain myles5000@gmail.com wrote:

My files are all created with a single fcs file. I was unaware of the cell percentage csv file though; that should give me the information I need.

On Tue, Mar 13, 2018 at 12:44 AM, MattMyint notifications@github.com wrote:

Hi, I'm able to reproduce this error by loading a cytofkit .Rdata file that holds the merged results of 13 fcs files (i.e. 13 samples). The error occurs when I select only one sample.

Basically, the heatmap generation step returns an error when trying to create a heatmap with just one column. Are each of your 30 data files created by analysing a single fcs file for each one?

The exact percentages can be viewed in the cytofkit output files. There will be a csv generated called "cytofkit__cluster_cell_percentage.csv" (e.g. cytofkit_Rphenograph_cluster_cell_percentage.csv)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/JinmiaoChenLab/cytofkit/issues/28#issuecomment-372553731, or mute the thread https://github.com/notifications/unsubscribe-auth/AarTZV8qaPG7xKOADd4oiyB8lI4eHNPxks5td1yugaJpZM4SctYi .

-- Emeka Fountain

-- Emeka Fountain

myles5000 commented 6 years ago

Can I generate that csv file again from the same data set if I accidentally overwrote it? My data set contains several fcs files and I previously had the file, but have since overwrote it with some data analysis.

On Tue, Mar 13, 2018 at 9:36 AM, Emeka Fountain myles5000@gmail.com wrote:

I'd meant to include this in the previous email, sorry: is there a way to generate that csv file for data files that use a single fcs file?

On Tue, Mar 13, 2018 at 9:34 AM, Emeka Fountain myles5000@gmail.com wrote:

My files are all created with a single fcs file. I was unaware of the cell percentage csv file though; that should give me the information I need.

On Tue, Mar 13, 2018 at 12:44 AM, MattMyint notifications@github.com wrote:

Hi, I'm able to reproduce this error by loading a cytofkit .Rdata file that holds the merged results of 13 fcs files (i.e. 13 samples). The error occurs when I select only one sample.

Basically, the heatmap generation step returns an error when trying to create a heatmap with just one column. Are each of your 30 data files created by analysing a single fcs file for each one?

The exact percentages can be viewed in the cytofkit output files. There will be a csv generated called "cytofkit__cluster_cell_percentage.csv" (e.g. cytofkit_Rphenograph_cluster_cell_percentage.csv)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/JinmiaoChenLab/cytofkit/issues/28#issuecomment-372553731, or mute the thread https://github.com/notifications/unsubscribe-auth/AarTZV8qaPG7xKOADd4oiyB8lI4eHNPxks5td1yugaJpZM4SctYi .

-- Emeka Fountain

-- Emeka Fountain

-- Emeka Fountain

MattMyint commented 6 years ago

Hi,

The csv file will be generated even if only one input fcs is provided. And yes, you can generate the same csv again with the same data set!

You may want to change the project name with each run so that you don't accidentally overwrite previous analysis.