When cell type proprotion plots are enabled, the default settings for proportions and the proportion comparision are set to the first metadata variable, which results in the message "Invalid selections for Cell Proportion Plot: "Proportions" and "Proportion Comparison" must be different". This is somewhat undesirable.
This could be solved by setting "proportion comparison" to the patient metadata variable, if such variable is provided in the config file. If not, this could simply be set to the second metadata variable. That will cause a error if the user only enters one metadata variable, however.
When cell type proprotion plots are enabled, the default settings for proportions and the proportion comparision are set to the first metadata variable, which results in the message "Invalid selections for Cell Proportion Plot: "Proportions" and "Proportion Comparison" must be different". This is somewhat undesirable.
This could be solved by setting "proportion comparison" to the patient metadata variable, if such variable is provided in the config file. If not, this could simply be set to the second metadata variable. That will cause a error if the user only enters one metadata variable, however.