Makes boxplot of log2-transformed counts for each target. Option to show target distributions relative to the LOD (LOD is subtracted from each data point, so LOD becomes the zero) and color boxplots by target detectability.
targetBoxplot(
data_matrix,
title = NULL,
sortBy = "median",
subtractLOD = FALSE,
blanks = NULL,
targetNoOutlierDetection = NULL,
horizontal = FALSE,
log2transform = TRUE,
replace_zero_LOD = FALSE,
axis_lab_normalized = TRUE,
excludeTargets = NULL,
excludeSamples = NULL,
colors = NULL,
detectHighColor = "pink",
detectLowColor = "blue",
showLegend = TRUE,
cex.targets = 0.4,
axis_limits = NULL,
match_matrix = NULL,
targets = NULL
)The Data matrix output from readNULISAseq.R or normalized data from normalization functions (targets in columns and samples in rows).
Title of the plot.
Order by which to sort the boxplots. Options are `'median'` for target medians, `'detect'` for detectability (must provide LODs). If `subtractLOD = FALSE`, will only sort by medians.
Should the target boxplot values be relative to LOD? Default is `FALSE`. If `TRUE`, will color boxplots by detectability.
A vector of column names that represent the negative controls. Required when `subtractLOD = TRUE`. This is passed to the `lod()` function.
Targets for which NC outlier detection should not be performed. Typically these are targets with no NC reads above 100. This is passed to the `lod()` function.
Should the boxplots be horizontal (target names along the y-axis)? Default is `FALSE` (target names along x-axis).
If TRUE (default), each value `x` will be transformed by `log2(x + 1)`. LOD values will also be transformed when `subtractLOD = TRUE`.
If TRUE (default is FALSE), will replace LODs of zero on the unlogged scale with zeros on the log scale. Probably only makes sense to use this option when using unnormalized data, because in this case LODs of zero become negative and when subtracted will cause shift upwards for the set of targets with LOD = 0. This option is only used when log2transform is TRUE.
If TRUE (default), will use "normalized count" for axis label. If FALSE, will use "count" for axis label.
Vector of names of any targets to exclude from the plots (such as internal controls).
Vector of names of samples to exclude from plots. These correspond to the column names.
Optional vector of colors that will be used to color the boxplots. Colors should be in the same order as the targets (rows) in the input data (after excluding any targets in `excludeTargets`). If provided, will override `detectHighColor` and `detectLowColor` when `subtractLOD = TRUE`. When `subtractLOD = FALSE`, default is `'grey'`
The color that represents 100 gradient color scale used when `subtractLOD = TRUE`. Default is `'pink'`.
The color that represents 0 gradient color scale used when `subtractLOD = TRUE`. Default is `'blue'`.
Should a legend appear in the plot? Only used when `subtractLOD = TRUE`.
Character expansion factor for target labels.
Matrix of indices provided by calcSampleTargetNAs. Lists samples/targets that should not be reported
Data frame containing target information including Curve_Quant attribute. If provided, target names with Curve_Quant == "R" will be prefixed with "* ".
Draws boxplots of target expression.