Troubleshooting PlotIndiv

Support
1

Hi team,

I am trying to run PlotIndiv on my PCA, CCA and PLS data. However, I see the following error message.

Error in $<-.data.frame(*tmp*, “pch.legend”, value = c(NA, NA, 2L, :
replacement has 1155 rows, data has 200
In addition: Warning message:
In shape.input.plotIndiv(object = object, n = n, blocks = blocks, :
‘ind.names’ is set to FALSE as ‘pch’ overrides it

And the code I have run is

plotIndiv(otus.pca, group= metadata_arcli$BMI,
title = ‘OTUs, PCA, comp 1 - 2’, legend=TRUE,
legend.title = ‘BMI’,
pch = as.factor(metadata_arcli$Sex),
legend.title.pch = ‘Sex’)

Could you please help me resolve this.

Thank you so much.

Regards,
Mrudhula

2

Hi @Mrudhula,

Try the following and let me know if your problem is resolved:

plotIndiv(otus.pca, group= metadata_arcli$BMI,
title = ‘OTUs, PCA, comp 1 - 2’, legend=TRUE,
legend.title = ‘BMI’,
pch = as.numeric(factor(metadata_arcli$Sex)),
legend.title.pch = ‘Sex’)

Please read plotIndiv documentation for pch for more info.

3

Thank you for your response @aljabadi.

I tried the code and I got the error again.

Error in $<-.data.frame(*tmp*, “pch.legend”, value = c(NA, NA, NA, :
replacement has 1155 rows, data has 200
In addition: Warning message:
In shape.input.plotIndiv(object = object, n = n, blocks = blocks, :
‘ind.names’ is set to FALSE as ‘pch’ overrides it

4

Hi @Mrudhula,

Do you have missing values in metadata_arcli$BMI? If that is the case ensure you replace them by a valid informative factor representing missing values. As a side note, ensure that the group argument (metadata_arcli$BMI here) is categorical and not continuous. That is, if you want to group by Body Mass Index, it is only possible if you bin BMI values first (e.g. BMI < 18, 18 =< BMI =< 25 etc).

5

Thank you for the respone.