This issue ended up being more multifaceted than originally thought.
--- Prior issue: ---
While exploring the bug, a separate (but related) issue was noticed. On standard (s)plsda objects (ie. non-MINT), only some of the background.predict() regions (or polygons) would display. Only thing that resolved this issue was manually adjusting the xlim and ylim parameters (increasing their bounds). This occured only for style = ggplot2. The ggplot2 package entirely removes polygons from the plot if a certain percentage of said polygon is outside the range of the axes (ie, if plot too zoomed in, polygon won't show). Previously internal_graphicModule() had used the bounds of the points as the default xlim and ylim, resulting in this cutoff.
Hence, to resolve this, if a background is supplied (and xlim/ylim are not supplied) to plotIndiv(), then the default value of the limit parameters is set to the average of the minimum/maximum values of the points and the polygons. This allows the plot to not be too 'zoomed out' as well as the polygons to be shown.
--- Immediate Issue: ---
The error raised when trying to use dist = "max.dist" in background.predict() on a mint.splsda object was caused by the absence of the center and scale attributes on the mint.splsda$ind.mat object. It had these for each study individually, but global values are needed for background.predict(). Using the follow externally would result in incorrect values for these attributes:
mint.res.object$ind.mat <- scale(mint.res.object$ind.mat)
Hence, mean_centering_per_study() was adjusted such that if the center and scale parameters were TRUE, irrespective of whether it is a MINT object or not, the global center and scale attributes will be appended to the ind.mat object.
--- Downstream issue: ---
The above fix resolved the error noted in Issue #24, however upon using the plotIndiv() function with a supplied background (on the mint.splsda object), no background would be shown. This was due to the absence of any code which handles background polygons within the if (style == "ggplot2-MINT") block (starts on line 364 of internal_graphicModule()).
Hence, the code from the if (style == "ggplot2") which handles backgrounds was copied over into the MINT block. On top of this, plotIndiv.mint() was slightly adjusted so the names(background.object) are converted into colours. This is how it is handled in the standard sPLSDA case so this process was homogenised for consistency's sake.
This issue ended up being more multifaceted than originally thought.
--- Prior issue: --- While exploring the bug, a separate (but related) issue was noticed. On standard
(s)plsdaobjects (ie. non-MINT), only some of thebackground.predict()regions (or polygons) would display. Only thing that resolved this issue was manually adjusting thexlimandylimparameters (increasing their bounds). This occured only forstyle = ggplot2. Theggplot2package entirely removes polygons from the plot if a certain percentage of said polygon is outside the range of the axes (ie, if plot too zoomed in, polygon won't show). Previouslyinternal_graphicModule()had used the bounds of the points as the defaultxlimandylim, resulting in this cutoff.Hence, to resolve this, if a background is supplied (and
xlim/ylimare not supplied) toplotIndiv(), then the default value of the limit parameters is set to the average of the minimum/maximum values of the points and the polygons. This allows the plot to not be too 'zoomed out' as well as the polygons to be shown.--- Immediate Issue: --- The error raised when trying to use
dist = "max.dist"inbackground.predict()on amint.splsdaobject was caused by the absence of thecenterandscaleattributes on themint.splsda$ind.matobject. It had these for each study individually, but global values are needed forbackground.predict(). Using the follow externally would result in incorrect values for these attributes:mint.res.object$ind.mat <- scale(mint.res.object$ind.mat)Hence,
mean_centering_per_study()was adjusted such that if thecenterandscaleparameters wereTRUE, irrespective of whether it is a MINT object or not, the globalcenterandscaleattributes will be appended to theind.matobject.--- Downstream issue: --- The above fix resolved the error noted in Issue #24, however upon using the
plotIndiv()function with a supplied background (on themint.splsdaobject), no background would be shown. This was due to the absence of any code which handles background polygons within theif (style == "ggplot2-MINT")block (starts on line 364 ofinternal_graphicModule()).Hence, the code from the
if (style == "ggplot2")which handles backgrounds was copied over into the MINT block. On top of this,plotIndiv.mint()was slightly adjusted so thenames(background.object)are converted into colours. This is how it is handled in the standard sPLSDA case so this process was homogenised for consistency's sake.