Error in generating plot for "Gini coefficient"
KashingTang opened this issue · comments
I am using immunarch verison 0.9.0,
R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)
Using the command " repDiversity" and "vis ", I can generate plots using methods like chao1, hill, div, inv.simp, d50.
But when I try to use the 'gini' method, I get an error.
Exact MiXCR commands
div_gini <- repDiversity(immdata$data, "gini")
vis(div_gini)
MiXCR report files
Error in UseMethod("vis") :
no applicable method for 'vis' applied to an object of class "c('immunr_gini', 'matrix', 'array')"
Hi, this issue is not related to MiXCR, but rather to immunarch. If you're looking to calculate and plot diversity metrics, there's no need to rely on any standalone packages, since MiXCR includes capabilities for downstream analysis. You can read more about it here. Please let me know if you have any questions regarding the postanalysis features of MiXCR.
Thank you for your prompt response and suggestion.
And sorry for asking in the wrong place.
I will try the downstream analysis features of MiXCR. Thank you again.