unable to run %>% commands

[GreyRockIQ]

Hello I am unable to run following codes on Seurat R 4.0 version

pbmc.markers %>% group_by(cluster) %>% slice_max(n = 2, order_by = avg_log2FC)

Errors as: Error in pbmc.markers %>% group_by(cluster) %>% slice_max(n = 2, order_by = avg_log2FC) : could not find function "%>%"

pbmc.markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_log2FC) -> top10 DoHeatmap(pbmc, features = top10$gene) + NoLegend()

Errors as: Error in pbmc.markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_log2FC) : could not find function "%>%"

Any suggestions? Thanks GreyRock

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. %>% is the magrittr pipe. Did you load the dplyr package indicated at start of vignette? That should import the magrittr pipe for use without actually loading magrittr too. Alternatively can just load magrittr.

Best, Sam

[Pancreas-Pratik]

Not a member of dev team either, but I think if you just throw:

`%>%` <- magrittr::`%>%`

at the beginning of your script, and run the command, it will add %>% functionality to your environment. (I like to do it this way, rather than loading the whole magrittr via library(magrittr) or the whole tidyverse via library(tidyverse))

If that doesn't work you might first have to install magrittr by using the following command:install.packages("magrittr") or install the larger tidyverse package that contains magrittr: install.packages("tidyverse"), and then either one of the 3 options above.

EDIT: It might be easiest to just load dplyr on second thought as is in the standard Seurat workflow cause I think group_by() and top_n() are apart of that, and you won't be able to run those commands without getting dplyr into your script... the easiest way is to just do: library(dplyr) at the beginning of your script.

[GreyRockIQ]

Thanks Samuel-marsh and Pancreas-Pratik for suggesting.. Reloading tidyverse and dplyr before script run solved first set of script for table but the second set is still on issue even after reloading dplyr with error commands below:

Error in UseMethod("group_by") : no applicable method for 'group_by' applied to an object of class "function"

[samuel-marsh]

@GreyRockIQ can you post the full code you are running that leads to error?

[GreyRockIQ]

Here is the full code..

pbmc.markers %>% 
  group_by(cluster) %>%
    top_n(n = 10, wt = avg_log2FC) -> top10
Seurat::DoHeatmap(pbmc, features = top10$gene) + Seurat::NoLegend()  

Error in UseMethod("group_by") : no applicable method for 'group_by' applied to an object of class "function"

[samuel-marsh]

Hi @GreyRockIQ

Assuming pbmc markers is an output from FindAllMarkers I ran your exact code using pbmck object from SeuratData and have no such errors. I would reccomend restarting your R session and re-running code and see if error persists. If so can you please post entire code you are running and output of sessionInfo

Best, Sam

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