PCA: selecting only certain groups, samples inconsistent

[sneumann]

Hi, we got a report in:
Today, I found a bug in Metfamily devel. In the PCA, when I selected only for certain groups, the samples that showed up were not consistent between the panel on the left right and individual samples. I have attached the supporting files in the attachment.

=> Indeed on the left the group "Water cultivated" is selected, and the tooltip on the right says "Infected wild". Similar below:

[sneumann]

So my hypothesis was that there is an indexing issue with the datastructure keeping the information for the PCA Tooltip after subsetting: in the sample table we have e.g. samples 1..70. Those 70 sample informations are used for the tooltips. If subsetting the first two groups, the tooltips still look correct. If subsetting the 1st and 3rd group, the first look good, but the 3rd group has labels coming from the 2nd group. Proposed solution: we need the same subsetting in the tooltips that we also have for the actual data matrix. Alternatively, the indexing for the tooltips should be by sample name, and not index position. Yours, Steffen

Places to continue checking:

MetFamily/MetFamily/app_files/server_guiTabPca.R

Line 608 in 22b0f1f

#dataColumnName <- dataList$dataColumnsNameFunctionFromGroupNames(groups = filterPca$groups, sampleNamesToExclude = dataList$excludedSamples(dataList$groupSampleDataFrame))[[minimumIndex]]

## compile information
  dataColumnName <- filterPca$sampleSet[[minimumIndex]]
  #dataColumnName <- dataList$dataColumnsNameFunctionFromGroupNames(groups = filterPca$groups, sampleNamesToExclude = dataList$excludedSamples(dataList$groupSampleDataFrame))[[minimumIndex]]

The commented line might hint what solution could be needed.
Yours,
Steffen