'silhouetteRankTest' not found

[yingmuzhi]

Hi, there, I appreciate your work about Giotto and I install the Giotto 1.1.2 using remotes::install_github("RubD/Giotto"). But when I am running the code below,

spatial_genes=silhouetteRankTest(visium_brain, 
                                 overwrite_input_bin=F, 
                                 output=file.path(dir.output, "sil.result"), 
                                 matrix_type="dissim", 
                                 num_core=20, 
                                 parallel_path="/usr/bin/parallel", 
                                 verbose=T, 
                                 expression_values="norm", 
                                 query_sizes=10)

It raise an error,

Error in silhouetteRankTest(visium_brain, overwrite_input_bin = F, output = file.path(dir.output,  : 
  could not find function "silhouetteRankTest"

could you please help me solve this problem, thanks.

[yingmuzhi]

The error also occurs when I type the following code into the R language interpreter,

> Giotto::silhouetteRankTest
Error: 'silhouetteRankTest' is not an exported object from 'namespace:Giotto'

[RubD]

@yingmuzhi Which version of Giotto are you using? silhouetteRankTest has not been updated to the latest version of Giotto (> v3)

[yingmuzhi]

Hello, @RubD Thanks for your replay. I am using Giotto 1.1.2 I guess.

> packageVersion("Giotto")
[1] '1.1.2'

The command remotes::install_github("RubD/Giotto") was used to install Giotto and devtools::install_github("drieslab/Giotto@master") was also tried. How to reinstall the latest version of Giotto > v3?

[yingmuzhi]

This command do me a favor

library(remotes)
remotes::install_github("RubD/Giotto@suite") 

and,

> packageVersion("Giotto")
[1] '3.3.0'

> Giotto::silhouetteRankTest
function (gobject, expression_values = c("normalized", "scaled", .........

That is pretty cool.