This vignette showcases some of the plot outputs generated with
mpwR and provides further explanations to the user.
The overview and individual plots apply both to absolute and relative
comparisons. In the examples, absolute numbers are used. In detail,
three workflows are compared on protein-level based on three replicate
The stacked barplot is an overview plot. “Complete” profiles refer to
identifications (IDs) present in each technical replicate. “Shared with
at least 50%” refers to IDs, which are present in at least 50% of the
technical replicates and which are not present in all replicates.
“Unique” refers to IDs, which are only present in one replicate run. An
additional category, which is not displayed in the example plot, is
“sparse”, which refers to a presence in more than 1 replicate and less
than 50% of the replicates.
For each respective workflow an individual barplot can be generated to
further highlight details of the presence of IDs. The example shows the
number of protein IDs in dependence of missing values for workflow A. In
detail, 294 IDs have no missing values (are present in each technical
replicate), 4 IDs have one missing value (are present in 2 technical
replicates) and 6 IDs have two missing values (are present in only one
Cumulative density plot
The cumulative density plot is used to display the coefficient of
variation (CV) for retention time (RT) and for label-free quantitation
A radar chart is used to highlight a relative comparison in percentage
across categories. In this example, the number of achieved protein IDs
are compared across three laboratories: LabA, LabB, LabC.