Append to neuronlist with rbind()?

[Shruthi Ravindranath]

Hello, 

I have a collection of neurons in .swc format registered to the same template brain. I want to read them all into a common neuronlist to facilitate plotting and other common operations on this data frame. Is this possible to do using read.neuron() and the R function rbind()? 

I tried this with no success:

all_nlist <- read.neuron(fw_neurons[1]) #fw_neuron is a list containing the paths to my .swc files of interest

for (f in fw_neurons[2:length(fw_neurons)]) {n1 = read.neuron(f) 

all_nlist <- rbind(all_nlist, n1)

}

When I try plot3d() with the above all_nlist I get errors that look like this:

In xyz.coords(x, y, z, xlab = xlabel, ylab = ylabel, zlab = zlabel,  ... :

  NAs introduced by coercion

Thanks for the help, 

Shruthi

[Gregory Jefferis]

Thanks for your question. Please use read.neurons to read in multiple skeletons to a single neuronlist object. If you had to combine multiple neuronlist objects manually you would use c(), which is the standard r way to concatenate lists and vectors. 

Can I suggest reading this article with worked examples 

https://jefferis.github.io/nat/articles/neurons-intro.html

I think it will repay the time investment. 

Best wishes,

Greg.

Sent from my iPhone

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[Shruthi Ravindranath]

Thanks a lot for the help. read.neurons() works well for my purpose.

On Friday, June 14, 2019 at 9:02:41 PM UTC-4, Gregory Jefferis wrote:

Thanks for your question. Please use read.neurons to read in multiple skeletons to a single neuronlist object. If you had to combine multiple neuronlist objects manually you would use c(), which is the standard r way to concatenate lists and vectors. 

Can I suggest reading this article with worked examples 

https://jefferis.github.io/nat/articles/neurons-intro.html

I think it will repay the time investment. 

Best wishes,

Greg.

Sent from my iPhone

On 15 Jun 2019, at 01:05, Shruthi Ravindranath <shruthi.ra...@gmail.com> wrote:

Hello, 

I have a collection of neurons in .swc format registered to the same template brain. I want to read them all into a common neuronlist to facilitate plotting and other common operations on this data frame. Is this possible to do using read.neuron() and the R function rbind()? 

I tried this with no success:

all_nlist <- read.neuron(fw_neurons[1]) #fw_neuron is a list containing the paths to my .swc files of interest

for (f in fw_neurons[2:length(fw_neurons)]) {n1 = read.neuron(f) 

all_nlist <- rbind(all_nlist, n1)

}

When I try plot3d() with the above all_nlist I get errors that look like this:

In xyz.coords(x, y, z, xlab = xlabel, ylab = ylabel, zlab = zlabel,  ... :

  NAs introduced by coercion

Thanks for the help, 

Shruthi

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