displayr / flipdimensionreduction Goto Github PK

Hi there,

Thanks a lot for this awesome package.
I was trying to apply CorrespondenceAnalysis to my toy dataset and I got the warning message below :
Warning messages: 1: In max(cumDim[cumDim <= lstats]) : no non-missing arguments to max; returning -Inf 2: In max(cumDim[cumDim <= lstats]) : no non-missing arguments to max; returning -Inf

Also the plot is really missing. However, when I use the "Principal" normalization, everything works fine.

Thanks!!

I have installed flipDimensionReduction R package v1.2.14 and when I try to use the UMAP algorithm I get the error "Algorithm not recognized" . I have also reviewed the source code here: https://github.com/Displayr/flipDimensionReduction/blob/master/R/dimensionreductionscatterplot.R and it appears that there is no logic for the UMAP algorithm.

Is this an oversight or did you drop support for the UMAP algorithm (which by the way I have used from your older package for many years successfully) . The package documentation still lists UMAP as one of the algorithm options.

Thank you for your contributions to this very important topic!

This is a question on objects created from this package: object of class "c('2Dreduction', 'tSNE')" I have a script that when run inside RStudio renders this object class as a nice interactive plot that I can export as a Web Page and share with others. I was hoping I could do this in a script running outside of RStudio as well.

However, when I tried using the 'htmlwidgets' package to save a 'tSNE_p05' object I get an error as follows:

 htmlwidgets::saveWidget(as.htmlwidget(tSNE_p05), file="C:/CWorkspace/temp/tSNE_p05_widget.html")

Error in UseMethod("as.htmlwidget") : 
  no applicable method for 'as.htmlwidget' applied to an object of class "c('2Dreduction', 'tSNE')"

Is there a recommended way of creating the interactive web page of the t-SNE plot? Any feedback is greatly appreciated.

Best regards
Ioannis

I realise this isn't really an "issue" and is probably a stupid question, but I'm new to R and am having a hard time reading the code.
Is x a matrix of indexed residuals? Counts? Proportions?

In the DisplayR documentation, the focus is set on the aspect ratio equal to 1 in order to have a good interpretation of the map.
however, when I create the map with CorrespondenceAnalysis function, the scale in Dim1 is bigger than the one in Dim2.
Is there an option to set the apspect ratio to be equal to 1?
Thanks!