Week #2 - General Discussion Thread

[DavidRach]

Welcome to Week #2, where we walk through the sometimes frustrating experience of trying to tell your computer via R where to find the experiment .fcs files you literally see in the folder in front of you.

This is the general discussion thread, for specific questions, open a new discussion in the Q&A section. Thanks! Best- David

[claude-chew]

Hi David,

This may be a silly question, but for Problem 2 of homework, are you looking for something different than list.dir() to retrieve the individual directory folders? It is highly likely that I am just not understanding this problem at all.

Thanks,
Claude

[jttoivon]

Hi,

I'm also confused about problem 2. To be more exact, the part that says 'that would retrieve the “” individual directory folders.' Is there supposed to be something between those double quotation marks?

Jarkko

[DavidRach]

Hi @claude-chew and @jttoivon, sorry for the unclear question! What I would be looking for would a function that would be able to isolate lets say either data or Cytometry in R from the following file path:

C:/Users/JohnDoe/Documents/CytometryInR/course/02_FilePaths/datra/target3

Similar to the case of how basename() would return target3

[claude-chew]

Sounds good, thanks for the clarification!

[NatalieRiddell]

Hi David, i'm struggling to copy files to a USB stick. I've assemble file paths for both my target location (folder in d drive) and my fcs file location within the target 2 folder/data/week2. I've updates the fsc files by switching the full.name argument to true. But the copy function didn't work:

[claude-chew]

Hi @NatalieRiddell , I'm going to attempt to field this and hopefully not mislead you, but partly because I want to see if I have enough of a grasp now to help someone else. @DavidRach can correct me if I am totally wrong!

So what I ended up having to do is create a list of the FCS files to copy and then tell it to copy. Here's my code (obviously with my own filepath etc. that you'll need to modify):

FCSTargetFolder <- "F:/TargetFolder"
FCS <- list.files("C:/Users/claud/OneDrive - Baylor College of Medicine/Documents/Week2/data", pattern=".fcs$", full.names=TRUE, recursive = FALSE)
library(stringr)
str_detect(FCS, "fcs")
FCS[str_detect(FCS,"fcs")]
FCSFiles <- FCS[str_detect(FCS, "fcs")]
file.copy(from=FCSFiles, to="F:/TargetFolder/")

Let me know if that helps,

Thanks,
Claude

[DavidRach]

@NatalieRiddell, within file.copy(), the from should be only file.paths of fcs files. The warning in the screenshot is likely because it is being passed folders instead of files. To fix that, either filter using the pattern=".fcs" argument in list.files(), or the stringr package str_detect approach (as @claude-chew did above). Also note it's currently showing for file.copy from=FolderLocation1 instead of files_present, not sure which intended to use.

The to argument should be to the folder on your usb drive. Often on Windows, that will be a file.path("F:", "ThisFolder").

Make sure you are within your working directory before trying to copy (getwd()) and that the various folders are accounted for in the full.names. So if trying to move target2 folder files, the file.names should show up as "data/target2/fcsfile1.fcs"

To get at the file.paths to the files within target2, you would need to generate list.files with path set as "data/target2" and full.names set to True to grab the full file paths.

One other possibility if the above doesn't work, is if your folder above week-2 is actually called @rcourse. If that is the case, you might be trunning into issues due to the special character @. Check the other two options first before renaming it, as don't want to break any established git paths.

Best,
David

[NatalieRiddell]

Hi Claude and David, after some playing around, and changing my folder name from @rcourse to rcourse, I finally copied my files to the target folder following Claude's advice- Thank you!

[DavidRach]

And @claude-chew , good job on the file.paths explanation ✔️ Only modification would be to try building dynamically using file.paths vs. hard-coded slashes

[claude-chew]

Thanks, appreciate it!

[Josefinebech]

Hi. When I try and do the Commit and Push step I get the following message. How do I proceed?

[DavidRach]

https://umgcccfcsr.github.io/CytometryInR/course/00_Git/#username-and-useremail

[Josefinebech]

Hi David. Thank you that worked. However, it seems like it never finish the commit. The program keeps loading after I press commit.

[DavidRach]

Hi @Josefinebech, I have seen that stalled commit a couple times. Try shutting down Positron and reopening, remake the commit if need be. Do make sure you are in your own project folder (Week 2) or the CytometryInR project folder before commit-ing, as you should only be making commits within your own project folders (to avoid issues bringing in new data each week).

Best-
David

[dennisaffram]

Hi David,
Week #2. I get this message after I do the PULL. I cannot find the .FCS files.

[DavidRach]

Hi @dennisaffram, are you in your own project folder (Week 2) or the CytometryInR project folder.

If you are in CytometryInR folder, you shouldn't be making changes in this folder 😄 If you hover over the staged changes you will get a backtrack arrow. Undo all changes until nothing appears within that screen, and then try pull again.

If you are in your own (Week2) you need to make a commit message for the changes you have staged, at which point you should be able to pull in anything from your GitHub repository, and then push.

Best-
David

[Oscar-Kai]

Dear David,

When creating "New Folder from Git" in Positron and copy paste the "https://github.com/Oscar-Kai/Week_02" a red pop feedback says " A git repository URL was not provided"

How do i go about this?

Oscar

[UMGCCCFCSR]

Hi @Oscar-Kai still traveling back from the conference, I will get to most of your questions tomorrow. This one we encountered with some of the in-person participants, for some weird reason, if you copy paste the url with your mouse, it won't work, but if you type the url in by hand, or alternatively Ctrl + C and then Ctrl + V to copy-paste the url via the keyboard, it is accepted without any issue. Not sure what bug is causing it on the Positron software side, as only a few people encounter it (and sporadically for certain urls on my computer). Best- David

[Oscar-Kai]

worked thanks

[Oscar-Kai]

Dear David,

When i run list.dirs() many files come on instead of what you are showing on the rirght of the picture compaireto what i generate on the left .

Is that expected or am I missing something here?

[UMGCCCFCSR]

Hi @Oscar-Kai, screenshot not appearing on my end, can you retry posting it?

For returning too many files, a couple possible reasons:

1. more files are present within the folder on your computer than what was originally present in the course folder (you can rule this possibility out by checking via Windows File Explorer, if there are only a couple, proceed to the next possibility). If there are more files present, as long as they are not similarly named, it shouldn't affect things.

2. the recursive argument was left on, if you just want to search within a particular folder (not the subfolders underneath), it should be set to false

list.dirs(path=".", full.names=FALSE, recursive=FALSE)

Let me know if either works, will circle back tomorrow.

Best-
David

[Oscar-Kai]

Hi@David,

even when i do

list.dirs(path=".", full.names=FALSE, recursive=FALSE)

I only see this:

Instead of what you show: