NEWS.md

In jmw86069/jamma: MA-plots for omics data

jamma 0.0.34.900

• Added dependency ggh4x to handle facet fill color. In future, it may provide improved faceting options, groups, multiple layers, etc.

bug fixes

• ggjammaplot()

• fixed error with missing colnames(x) or rownames(x)

updates

• Bumped jamba version dependency to 0.0.104.900 to support SparseMatrix objects as with SingleCellExperient and Seurat matrix data.

• centerGeneData()

• Updated to add includeAttributes=FALSE with jamba::rowGroupMeans().

• Added tests to all basic use cases, and to cover SparseMatrix input.

• jammaplot()

• Removed argument ma_method, it was deprecated.

• Added argument apply_transform_limit=40 to apply jamba::log2signed() when any value is above this threshold, only when useRank=FALSE.

• ggjammaplot()

• Added argument apply_transform_limit=40 to apply jamba::log2signed() when any value is above this threshold, only when useRank=FALSE.

• Now uses ggh4x::facet_wrap2() to apply color to facet strips.

internal functions removed

• element_textbox_colorsub(), element_grob.element_textbox_colorsub() were removed, in favor of using ggh4x functions for ggplot2 facet strip color fill.

jamma 0.0.33.900

changes to existing functions

• jammaplot()

• A warning was shown "Warning in min(x, na.rm = na.rm) : no non-missing arguments to min; returning Inf" which was caused by xlim not being defined for each plot panel, thereby causing ablinesV to throw an error because no values fit within the undefined x-axis range. Now when xlim argument is not provided, it uses the range of x-axis values from jammacalc() for each panel.

• This change makes panel x-axis ranges more consistent by default. They should have been consistent already, but in some cases NA values caused the range to differ slightly from panel to panel. In most cases, it caused no visible effect in x-axis labels.
• This change also allows samples within centerGroups groupings to have distinct x-axis ranges, since each individual group can represent potentially very different values depending upon the experiment.

jamma 0.0.32.900

bug fixes

All instances of if (class(x) %in% c("a", "b")) were corrected to use format compatible with R version 4 which considers this syntax an error and not a warning. New format is if (any(c("a", "b") %in% class(x))).

• jammaplot(), update_list_elements(), centerGeneData(), ggjammaplot()

• Fixed if statement logic to remove length=2 error in all scenarios.

other changes

• jammaplot()

• argument help docs were updated for clarity.

• change argument default to filterNeg=FALSE, although this argument is deprecated and only used when ma_method="old". The change was made to reflect the current default behavior which uses noise_floor=0 and noise_floor_value=NA, which replaces all values at or below 0 with NA, causing these values not to contribute to the data centering and MA-plot output.

jamma 0.0.31.900

changes to existing functions

• jammaplot()

• New argument outer_margins to control the whitespace around the outside of the MA-plot panels, only when doPar=TRUE.

• The y-axis labels are only shown on the first plot each row, and plot panels are condensed side-by-side.
• The default margins has much smaller left value, so plots can be placed closer side-by-side.
• Far very many MA-plot panels, the plot panels are much more visibly condensed, especially when useRank=TRUE, which previously increased each panel left margin by 2 lines; now it only increases the left outer margin.

jamma 0.0.30.900

changes to existing functions

• jammacalc()

• now inherits arguments controlFloor, naControlAction, naControlFloor consistent with centerGeneData().

• now calls matrix_to_column_rank() instead of calculating internally.

• jammaplot() and ggjammaplot()

• gained arguments controlFloor, naControlAction, naControlFloor consistent with centerGeneData(). These arguments are passed to jammacalc().

jamma 0.0.29.900

new functions

• matrix_to_column_rank()

• converts numeric matrix to column rank data, as used when useRank=TRUE.

• This function becomes its own standalone function so it can be called when necessary in other areas.

updates to existing functions

• jammacalc()

• calls matrix_to_column_rank() instead of calculating internally.

jamma 0.0.28.900

updates to existing functions

• centerGeneData()

• Note that default behavior is unchanged.

• New argument controlFloor to impose a minimum control summary value when the summary value is below controlFloor.

• New argument naControlAction used when all control sample values are NA:

  1. naControlAction="na": leave values centered values as NA (default behavior)
  2. naControlAction="row": center versus remaining non-NA row values
  3. naControlAction="floor": center versus numeric floor
  4. naControlAction="min": center versus the minimum observed value

• New argument naControlFloor=0 used only when naControlAction="floor". When zero, values are effectively un-centered. However, sometimes the range of signal is 20-35, in which case it may be practically more useful to use naControlFloor=20 so data is centered relative to the minimum range of detection.

• Added proper prefix to ggplot2::after_stat() for ggjammaplot().

testthis unit tests

• Began the process of covering package functions with unit tests. Currently: centerGeneData().

jamma 0.0.27.900

updates to existing functions

• ggjammaplot() was updated:

• Point density now shares the same range for all panels, including outlier panels. Previously, outlier panels generated their own color gradient, due to their specific numeric range of point density values calculated by ggplot on the fly. The new code will define the numeric range using non-outlier samples, then re-uses the same numeric range for outlier panels when there are outlier panels. This step appears to add some lag to rendering, although there is already more lag than with base R graphics.

• New argument detail_factor is a single argument to adjust the level of detail in the point density per facet panel.

• jammacalc()

• The calculation of rank data using rank(..., na.last=FALSE) was assigning ties to repeated numeric values, but was assigning unique (arbitrary, by order they occur) ranks to NA values. The new code secretly converts NA to the lowest numeric value so they are assigned tied rank values.

jamma 0.0.26.900

• volcano_plot() updates:

• Fixed bug where lfc_colname was used even when only fold_colname was appropriate for the data. It now properly uses the lfc_values internal vector for relevant steps.

• hi_points now accepts a list input, to color code different subsets of points different colors
• new argument hi_colors coincident with hi_points having list input: length(hi_colors) should match length(hi_points) so colors will be applied to each vector in the list. If no colors are assigned, then bright categorical colors will be defined by colorjam::group2colors().
• when hi_points is a list, a color key is placed at the bottom of the plot, making the bottom margin 2 lines taller, and shifting other captions up by 2 lines.

jamma 0.0.25.900

Main change: this version:

1. Automatic indication of controlSamples in each MA-plot panel.
2. Ability to supply custom names for each MA-plot panel.

updates to existing functions

• jammaplot()

• whichSamples accepts character or numeric and will subset itself to match available names(x) or nsamples accordingly.

• New argument sample_labels to provide custom labels for each sample without having to rename colnames(x) in the process. An example has been added.

• New argument controlIndicator:

  • "titlestar" - asterisk appended to the title of each plot
  • "labelstar" - asterisk labeled inside the top corner of each plot
  • "none" - no indicator is drawn

• par("mar") is now only updated when doPar=TRUE.

• New argument panel_hook_function to supply a custom function to be run after drawing each plot panel. An example has been added, showing how to draw a box around each figure.
• y-axis labels are drawn using format(..., big.mark=",") as an improvement for useRank=TRUE.

• Margins have been adjusted so the title box default above each plot has more room when there is no maintitle that would otherwise have added space to the top of each overall figure.

• find_colname() is now exported.

• added log2fold_to_fold() and fold_to_log2fold() functions as required by volcano_plot().

jamma 0.0.24.900

bug fixes

• volcano_plot() was throwing an error due to the new use of utils::modifyList(), ultimately caused by update_function_params(). That function was updated, resolving the error.
• jammaplot() was updated to pass panelWidth="minimum" to jamba::drawLabels() for the title box when using base R graphics plots. This change ensures the box is at least the plot panel width, and will be larger if the label is wider than each panel.

jamma 0.0.23.900

changes to existing functions

• jammaplot() title box labels are now placed above plot panels!

• This changes is being tested, but it seems like a sensible default not to obscure points in each plot panel.

• two new arguments: titleAdjPreset, subtitleAdjPreset
• passed to jamba::coordPresets() which defines coordinate positions in base R graphics context. The two main arguments are preset and adjPreset, where preset defines the coordinate "edge" or "corner" position, typically something like "top" or "bottomleft"; and adjPreset defines relative placement of the label. By default, adjPreset chooses the opposite orientation, to keep labels inside the plot panel. However preset="top" defines the top edge of the plot, and adjPreset="top" places the label above the top edge of the plot panel.

• The calculation of top outer margin is dependent upon the number of text lines in maintitle, and was increased to accomodate the new default placement of title box labels above the top panel. It does not account for multi-line title box labels, in that case, supply maintitle with empty extra lines at the end to add spacing.

• jammaplot() argument margins=c(3.5, 2, 0.3, 0.2) is typically good for non-ranked MA-plots. When useRank=TRUE the numbers typically have 4 or more digits, and need more space. In this case by default, margins + c(0, 1, 0, 0) is used.

bug fixes / improvements

• jammaplot() correctly represents highlightPch point shapes in the highlight point legend at the bottom, via outer_legend().
• outer_legend() when pt.bg=NULL it will adjust col slightly darker for point shapes ranging from 21 to 25, and will assign pt.bg=col so the fill color is correct.

jamma 0.0.22.900

new functions: volcano_plot()

The volcano_plot() function has been in use for a long time, but not in R package form. The sticking point has been the block arrows drawn in plot margins (outside the plot panel) which describe the number of points that exceed statistical thresholds. Colleagues seem to like having these block arrows with summary numbers, and they've appeared in some published papers. That said, sizing block arrows consistently for all plot aspect ratios has been tricky, and migrating everything to ggplot2 is on the short to-do list. Unclear how block arrows would work in ggplot2.

• volcano_plot() - Draw volcano plot, work in progress
• blockArrowMargin() - draws block arrows in plot margins
• gradient_rect() - draw rectangle with gradient color fill
• logAxis() - draw log-transformed -log10(pvalue) axis labels
• find_colname() - find colname matching a character string
• update_function_params() - update function arguments in place
• update_list_elements() - utility called by update_function_params().

immediate change to existing functions

• update_list_elements() appears to have identical purpose and functionality as utils::modifyList()

• update_function_params() was updated to call utils::modifyList()

• update_list_elements() is deprecated while this change is tested.

jamma 0.0.21.900

notable changes to default values

jammaplot() argument default filterFloorReplacement=NA:

• This change corrects an issue where the row mean was calculated using values that may contain a large proportion of zero 0, therefore pushing the x-axis position toward zero. The effect often also pushed the y-axis difference-from-mean to slightly larger magnitude, since the baseline value was typically closer to zero.
• The effect of the change in argument defaults is that the x-axis position of points displayed will reflect the mean/median of values above zero, and y-axis will reflect the difference from mean/median of values above zero, thus displaying mean and variation of those measurements that detected a signal, without being influenced by the proportion of those points that detected a signal.

• Specifics:

• noise_floor and noise_floor_value will replace deprecated arguments filterFloor and filterFloorReplacement, respectively. But the main change is to the default values.

• previous default: filterFloor=0 and filterFloorReplacement=filterFloor set any value at or below 0 to 0.
• new default: noise_floor=0 and noise_floor_value=NA sets any value at or below 0 to NA.
• The change mostly affects data with large number of zero 0 values.
• Points below noise_floor will no longer contribute toward the sample MAD factor, which should be correct as the default.
• The x-axis summary value, by default is the mean unless useMedian=TRUE in which case it uses the median, is calculated using the remaining measurements, above the noise_floor, so by default values above zero will be displayed in each plot panel.
• The assumption is that a measurement 0 is an absence of measurement, and therefore should not contribute to the mean for that row of data, nor to the variability (or absence of variability) for the sample column.

• The same assumption should hold true for values below zero, where upstream processing should in theory have generated negative values as a result of background subtraction/adjustment by appropriate methods. Negative values are therefore also considered "absence of measurement" and the specific numeric value has no quantitative meaning in this function.

• All that said, the previous behavior can be used with argument noise_floor_value=noise_floor.

• Finally, some case can be made that the points filtered may optionally be displayed, in order to indicate their presence in the data. This option may be enabled in future if it seems necessary.

• It is unclear how to plot points whose values were zero.

• If for example the non-zero mean x-axis position for a row is 12, does it imply the points at for this row would use x=12 and y=-12? Or should these points use x=0 and y=0?
• It seems more sensible not to display points whose measurements have been filtered from analysis - at least for now.

changes to make jammaplot() and ggjammaplot() consistent:

• ggjammaplot() was modified for consistency with jammaplot():

• colramp argument added

• outlierColor can be a color function, for example colramp="inferno" and outlierColor="inferno_r" will use the reverse color ramp for a nice visual effect.
• new argument fillBackground=TRUE optionally fills each plot panel with the first color ramp color, affecting outlier panels. Previously each plot panel has a small region around the outside that was not filled, due to ggplot2 axis range expansion slightly beyond the 2d density coordinates.
• MAD outlier panels were not properly recognized, the MAD values were displayed but the background was not highlighted with outlierColor. Issue has been resolved.
• noise_floor=0 is the new default value, consistent with jammaplot(). Any value at or below is set to noise_floor_value which by default is NA, but can be changed to noise_floor.

• The MAD factor text color uses a color that contrasts with the base color gradient used in each plot panel, using white text versus dark background for example. It calls jamba::setTextContrastColor(). Outlier text is either red or gold, as appropriate.

• jammaplot() was modified for consistency with ggjammaplot():

• New arguments noise_floor and noise_floor_value, which replace

• Deprecated arguments filterFloor and filterFloorValue.
• filterFloorReplacement=NA is the new default value, which may be a substantial change for data that contains a large proportion of missing values.
• The MAD factor text color uses a contrasting color, as with ggjammaplot().
• outlierColor="lemonchiffon" default, consistent with ggjammaplot(). It sounds yummy.

jamma 0.0.20.900

bug fixes

• jammaplot() was not properly passing argument assay_name to downstream function get_se_assaydata() when the input was SummarizedExperiment. It was by default always using the first assay stored in the SE object.

jamma 0.0.19.900

updates to package dependencies

Unfortunately the gridtext R package issue https://github.com/wilkelab/gridtext/issues/22 results in removing this package and ggtext as dependencies from jamma. The installation requires specific recent versions of GCC compiler that I have trouble resolving on my own linux servers. As a result, they are moved to Suggests and the corresponding jamma functions will handle them as optional.

jamma 0.0.18.900

Bumped dependency on jamba to version 0.0.66.900 to avoid error with rowMedians() that should use matrixStats::rowMedians().

Note: The pkgdown::build_site() failed due to SSL certificate expiration, apparently from the crandb.r-pkg.org site. The workaround is to set this option beforehand, which prevents pkgdown::build_news() from trying to access that URL. options("pkgdown.internet"=FALSE)

new functions

• ggjammaplot() - the ggplot2 equivalent to jammaplot(). See examples, there are a variety of example figures, using straight MA-plots, raw and normalized data, using subset of samples, and optionally highlighted points.

Still to-do: * when blankPlotPos is used, the plot itself should be empty, without grid lines * add subtitle to the bottom-left corner of each plot panel * use geom_text_repel() to label highlightPoints - should probably be optional. * more testing for large number of plot panels, for example test the aspect ratio for density and pixel size calculations

• element_textbox_colorsub() - a custom ggplot2 element that enables colored facet strip background colors using name-value pairs.

• The technique was based upon a post by Claus O. Wilke, and is the closest to a "true ggplot2" methodology that I found. Other alternatives involved using the gtable package, and modifying grob grid graphical objects directly. See stackoverflow questions/60332202/conditionally-fill-ggtext-text-boxes-in-facet-wrap

• Note that this function very likely will move into the colorjam package to become the default of colorjam::theme_jam()

• This function has not been tested with facet_grid() but in principle it should work.

• element_grob.element_textbox_colorsub() - required for the ggplot2 workaround with facet strip label background colors.

new dependency

• ggtext package is a dependency for ggjammaplot(), however it is a lightweight and useful package, whose dependencies are largely also in common with ggplot2.

jamma 0.0.17.900

changes to existing functions

• jammaplot(), jammanorm() and jammacalc() were updated to handle useMedian by default, but to accept useMean for backward compatibility.

jamma 0.0.16.900

changes to existing functions

• centerGeneData() has been changed to what was previously centerGeneData_new(), and the old function was renamed to centerGeneData_v1(). The new function is designed to be backward compatible.
• jammaplot() now accepts SummarizedExperiment objects as input, used alongside new argument assay_name which determines the matrix to use for MA-plots. The assay_name input can be an integer index, or by default it will use the first assay matrix in x. Alternatively to use the last assay matrix (if normalized data is stored in the last assay position for example) supply assay_name=Inf and the default will use the last assay in the list.
• jammacalc() now calls centerGeneData().
• jammanorm() help text was expanded.

Added various entries to TODO.md for future work.

jamma 0.0.15.900

bug fixes

• jammaplot() fixed issue when applying filterFloor and useRank=TRUE, it was converting to rank before applying filter floor. An edge case but important for count data, where using filterFloor=0 and filterFloorReplacement=NA is useful, and using useRank=TRUE is informative especially when using methods like DESeq2/edgeR downstream with count data.

minor updates

• jammacalc() new argument useRank so the conversion to rank happens inside this function, as it should.
• Added some package prefix to functions such as jamba::nameVector(), `jamba::rmNA().
• Removed require(jamba) and require(matrixStats) in favor of using proper package prefixing, and check for matrixStats using rownames(installed.packages()).
• Cleaned up some R code, removing sections that were deprecated.
• Edited the wording for jammaplot() function parameters.

changes to existing functions

• jammaplot() cleaned up logic on handling colramp and colrampOutlier arguments.
• jammaplot() default ma_method="jammacalc" which is equivalent but slightly streamlines the internal calculations.

jamma 0.0.14.900

new function

• jammanorm() a basic normalization method that uses the output of jammaplot() or jammacalc(), and normalizes data such that the controlGenes are centered at y=0. In words, it makes the controlGenes have mean zero change from average across samples. It optionally takes pre-defined controlGenes (housekeeper genes), and optionally applies an expression minimum threshold, to ensure genes are expressed above noise.

jamma 0.0.13.900

changes

• jammaplot() argument default changed to useMean=TRUE to plot the mean centered value, instead of the median.

jamma 0.0.12.900

changes

• jammaplot() argument useRank=TRUE will produce the rough equivalent of a non-parametric MA-plot, where the y-axis unit is either the actual change in rank, or the fractional change in rank adjusted by the number of rows.

jamma 0.0.11.900

new functions

• outer_legend() is used to place a color legend outside multi-panel base R graphics, for example when using par("mfrow"=c(2,2)). By default it places the legend at the bottom, centered in the plot device. It of course may move to jamba but that package is already getting overloaded.

changes

• jammaplot() has transitioned from using groupSuffix to add a text suffix to each panel title, to using subtitle to display text in the bottom-left corner of each panel. In most cases, this change results in better use of whitespace on each plot, and helps keep the title label smaller.
• jammaplot() allows a list color ramps in the argument colramp, which applies a different color ramp in each panel.
• jammaplot() changed how highlightPoints are handled, making it more robust to different types of input, vector or list. Fix error when highlightPoints had no list name.

jamma 0.0.10.900

new functions

• jammacalc() is used to calculate data ready for MA-plots, to separate this logic from the jammaplot() function used for visualization.
• The jammacalc() function slightly improves upon the jammaplot() calculations by simplifying the centering by calling centerGeneData_new() (or centerGeneData()) instead of performing similar calculations itself. The results should be notably faster especially for larger data matrices.
• The jammacalc() function also changes the result of groupedX=TRUE, which now correctly uses each group median value instead of a median across the group medians. It allows each group of MA-plot panels defined by centerGroups to be completely independent of other groups, which has benefits and discrepancies that depend upon how the centerGroups values are defined relative to the intended downstream statistical comparisons. For example, we recommend centerGroups broadly include the sample groups that will eventually be compared, specifically so the distributions are directly compared in the MA-plot visualization. However, certain per-group QC checks are ideally performed by using centerGroups for each sample group. Overall, be aware of the effects of each scenario, and adjust the expectations and assumptions accordingly.
• jammaplot() new argument ma_method where ma_method="old" calls the previous code for MA-plot calculations, and ma_method="jammacalc" calls jammacalc() with the newer equivalent calculations.

changes

• Added "colorjam" to R package dependencies.
• Removed R package dependencies on "rgeos" and "sp".
• points2polygonHull() now uses grDevices::chull() instead of rgeos::gConvexHull(). The function accepts numeric matrix, data.frame, tibble, tbl, and SpatialPoints input, and can output either a two-column numeric matrix, or SpatialPolygons as output.
• the default argument to centerGeneData() was changed from "indata" to "x" to be consistent with Tidyverse syntax.

future changes to centerGeneData()

• centerGeneData() will soon be replaced by centerGeneData_new() after a period of testing. The functions should be equivalent. The new function uses jamba::rowGroupMeans() to produce the summary values used for centering. The change will consolidate the logic of calculating row group values into jamba::rowGroupMeans(), as opposed to duplicating only certain parts of that functionality inside centerGeneData(). The new function also surfaces outlier detection and removal during centering in one step. The potential downside, and need for a period of testing, is that the full input matrix is centered versus the expanded row group matrix in one step. Briefly there will be two matrices with identical dimensions, which will produce a higher memory profile. For extremely large matrices, this change may become problematic, and may require an alternative strategy during the centering step.

• jammaplot() will be refactored to streamline certain calculations using the newer centerGeneData_new().

jamma 0.0.9.900

changes to jammaplot()

• now creates a default groupSuffix based upon the centerGroups if any, the goal is to ensure the center groups are by default included in each panel label.
• Columns with missing data (e.g. all NA values) are now handled by plotting a blank plot panel with background color outlierColor. The MAD value is assigned Inf.
• now uses maintitle as the title for the overall set of plots, displayed in the top outer margin of each page. New argument maintitleCex controls title text size.
• the default input argument is changed from "object" to "x", to be consistent with other tidyverse-friendly workflows.
• attribute names are changed from "mvaMADs", "mvaMADoutliers", "mvaMADfactors" to "MADs", "MADoutliers", "MADfactors". The names using "mva" are deprecated and will be retired in a future version of jamma.
• outlier MAD label cex is now 0.9*titleCex, making the MAD label slightly smaller than the panel label.
• Outlier plot panels are now highlighted using >= outlierMAD, consistent with the formal outlier detection. Previously it was erroneously using > outlierMAD.
• new argument subtitleBoxColor which defines the background color for optional subtitles printed at the bottom of each plot panel. Used to color-code centerGroups, if groupSuffix="" and subtitle contains centerGroups as labels.

Notes

• Very likely, the base R plotting may be replaced or augmented by using ggplot2. Past reason for using base R were due to panel layout, and wanting detailed control over smoothScatter per-panel density plotting.

• In future, the centerGroups value may be displayed inside the subtitle label box at the bottom-left corner of each panel, color-coded to help indicate the centering group.

• In future, controlSamples may be indicated by appending an asterisk "*" at the end of the main label for each panel.

jamma 0.0.8.900

changes

• drawLabels() and coordPresets() were moved to the jamba package, consistent with the need for wider re-use among Jam packages.
• Added dependency on the version of jamba that includes drawLabels().

jamma 0.0.7.900

changes

• Based upon feedback regarding difficulty installing the "rgeos" package, changed jammaplot() to use grDevices::chull() when doHighlightPolygon=TRUE. The output should be identical, without the need to install the rgeos package.
• changed drawLabels() now uses label height to define the effects of boxCexAdjust on the label box size, making the x- and y-adjustment more consistent when using long labels; it also uses jamba::getPlotAspect() to correct for aspect ratio. Note it is probably far less useful to supply x and y values for boxCexAdjust.
• made adjustments based upon the single-line height and not the total string height, affecting multi-line labels.

jamma 0.0.6.900

new functions

• drawLabels() which draws a colored box with label inside, positioned by default at the center of the x and y coordinates provided. This function will be tested then moved to the "jamba" package.

changes to existing functions

• jammaplot() by default will use drawLabels() to print a label in each panel, instead of the previous method which used legend() and was not properly centered. In future, labels may detect whether to enforce word-wrap in order to keep labels from overlapping adjacent panels.

other changes

• pkgdown was added to the site documentation.

jamma 0.0.5.900

changes to existing functions

• jammaplot() had a fairly substantial shift in default behavior, concerning the x-axis coordinate when using centerGroups to center a subset of samples. Previous default was to use one global x-axis coordinate across all samples, regardless of the centerGroups. New default behavior is to calculate an x-axis value for each centerGroups so within each group the data is self-contained. This behavior can be controlled with groupX=TRUE which applies grouping to the x-axis, and groupX=FALSE for the previous behavior. I admit, this change has pros and cons. On the one hand, there is inherent benefit for keeping each subset grouping independent, with the possible downside that comparisons across groupings may not be visible.

jamma 0.0.4.900

enhancements

• Bumped the version number to cover a few smaller updates.

jamma version 0.0.3.900

enhancements

• jammaplot() now more consistently handles highlight point parameters, where each are expected in list form: highlightPoints, highlightPch, highlightCex, and highlightCex. If highlightPoints is sent as a vector, it is converted to a one-vector list. If highlightPoints is a list, then the other parameters are converted to list as needed (as.list()) and expanded to length(highlightPoints). This way, each highlight set of points can have custom color, size, and shape, to help visually discern them.

jamma 0.0.2.900

new functions

• centerGeneData() the main tool for calculations by jammaplot(), centers data by subtracting the row mean or median; optionally within groups of columns; optionally with specified control columns per group.
• jammaplot() the main MA-plot function.
• points2polygonHull() takes a set of points and draws a polygon hull encompassing them. It calls rgeos::gConvexHull(). The function is intended to indicate the location of highlighted points on each MA-plot panel.

modifications

• several default settings were changed for jammaplot(): larger titleCex; outlierColramp is NULL, in favor of using outlierColor to change only the first color from colramp.

jmw86069/jamma documentation built on Oct. 11, 2024, 7:08 a.m.