TODO.md

In jmw86069/jamma: MA-plots for omics data

TODO for jamma

07oct2024

• DONE. Fix ggjammaplot() bug where ggplot2 facet strip background color no longer applies titleBoxColor properly. Unclear when this stopped working, probably something in the ggplot2 3.5.x update.

• Fix was to use ggh4x::facet_wrap2() to apply color and fill to ggplot facet strip rectangles.

• Enable subtitle arguments for ggjammaplot() consistent with jammaplot().

17sep2024

• Add support for SingleCellExperiment/Seurat objects.

• Adopt similar mechanism used in jamses::heatmap_se()

• Use rowRanges() when necessary.

• Update centerGeneData() to handle Matrix objects, not just matrix

• for example, SingleCellExperiment data may provide dgCMatrix

• inherits(x, "sparseMatrix") is valid for Matrix sparse matrices, and sparseMatrixStats may provide equivalent methods to matrixStats if installed.

• Check if matrix is sparse, check if sparseMatrixStats is installed, if so use sparseMatrixStats::rowMedians(), otherwise apply(x, 1, median)

• Consider subtitle ability to use colData() colnames.

• Consider colorSub to define colors used by arguments titleBoxColor and subtitleBoxColor.
• Add asterisk to corner of ggjammaplot() output

14aug2024

• Consider other data centering options:

• Use case:

  • Compare GroupA to GroupB and GroupC.
  • Goal is to show up-regulated genes in GroupA.
  • Center versus GroupA shows everything down in GroupB/GroupC.
  • Centering by GroupB/GroupC uses the mean of GroupB/GroupC.
  • Proposal is to center by group "min" or group "max" instead of group "mean".
  • Possible to accomplish with rowStatsFunc argument?

  • If the goal is a heatmap, jamses::heatmap_se() could accomplish it entirely with custom code:

    • Define custom rowStatsFunc function that recognized colnames, assigned them to groups, returned the appropriate group stat (min, max, mean, median).
    • It also needs to label the centering accordingly. Entirely specific to heatmap_se(). Or is it?

• Consider including attributes which describe the centering.

  • Method: mean/median
  • controlSamples
  • centerGroups
  • Optional labels? control_label, centerby_label

• Consider method which accepts SummarizedExperiment data, and arguments:

  • assay_name - if one value, one matrix is returned, otherwise list
  • centerby_colnames - to define centerGroups
  • controlSamples - same as usual, to define controls for centering
  • Output includes attribures including consistent centering label, to be used by MA-plots, jamses::heatmap_se() and other tools.

09jul2024

• Consider RLE plot - which is a flattened form of MA-plot

• Motivation: single cell data with thousands of columns, they should not become independent panels.

• Could be useful for bulk 'omics data by providing a quick global view.
• "Problem samples" could be expanded to show the full MA-plot.
• For reference see https://davislaboratory.github.io/GeoMXAnalysisWorkflow/articles/GeoMXAnalysisWorkflow.html the plotRLExpr() function shows example before and after normalization.

• Weakness of this style is that it doesn't show non-linear MA-plot, however the box-whisker/median with range is effective at showing when one sample has much different variability than others.

• Consider adding signed-significance plot, perhaps ssplot()

• Goal is to provide two data.frame objects that have identifiers (gene?) that can be aligned to one another.

• Each data has significance column (adjusted P-value, P-value, Q-value, FDR) and a directional column (fold change, log fold change, ratio, etc.).
• The -log10(significance) * sign(fold) is used for each axis.
• Statistical thresholds are drawn for each dataset, usually P-value threshold. Shown as dotted/dashed lines on respective axes.
• Consider option to impose fold change threshold for each data also?
• Consider option to use log fold change on each axis.

30may2024

• volcano_plot()

• return data.frame equivalent to the data plotted, make it easy to find hits, and highlighted points.

13mar2024

• Consider how to utilize colData() sample annotations.

• Go with "easiest thing that works" since in most cases, MA-plots are data-agnostic QC for technical quality assessment. However, centering within known sample annotations could be convenient.

• For example: colorized subtitle boxes, or augmented labeling.
• Situation is that SummarizedExperiment input offers more sample annotations than are easily added via subtitle.
• Could mimic arguments in jamses::heatmap_se(): centerby_colnames, colData_colnames.
• Could apply sort order to samples by argument colData_byCols, pass to: mixedSortDF(colData(se), byCols=colData_byCols)
• New argument sample_color_list, optional color assignment for colData columns.

27sep2023

• develop better method to organize MA-plot panels

• for example columns organized by batch

• generally some assignment of sample to panel number

01aug2023

• centerGeneData()

• Enable SummarizedExperiment input, either as a separate function, or as option for this function. It should require assay_name, and return a numeric matrix.

• Figure out a reasonable way to include experiment design factors in jammaplot() and ggjammaplot() panel labels.

• For example "BAH013760_101_NEG_MS1" is not a helpful identifier, it would be much more interesting to include "Male, Dex-Treated, Time 3".

• Bonus points for including each factor on its own line, using categorical colors for each value to make it easier to scan by eye.

• Fix missing strip text colors in ggjammaplot() when multiple colors are supplied for titleBoxColor.

• Somehow the ggplot2 element_grob() dispatch is not calling the custom functon element_grob.element_textbox_colorsub().

31jul2023

• DONE. Fix error ggjammaplot() when input data x does not contain colnames, or rownames. Either case produces an error.

19jul2023

• Some method to detect non-linear (non-horizontal) MA-plot signal

• Example case is one sample whose values are nearly all zero, the MA-plot looks like a diagonal line aiming down from left to right. After log-ratio normalization (for example with jammanorm()), the signal is shift up so the mean signal is at y=0, however the diagonal is still there.

• Simplest possible idea is to fit a line to points above the minimum threshold defined by mad_row_min, and test the slope.

• It is unclear how much to trust a linear fit, and assuming the linear fit is reasonably good, what to do with the slope afterward.

  • How much deviation from slope=0 is tolerable?
  • Should the range of acceptable slopes be data-defined?

• Another idea: Could jammanorm() only normalize using rows where the raw values are above the noise threshold mad_row_min? Currently the process uses the x-axis calculated value (row mean/median) to apply that threshold. Logically it seems reasonable that measurements below a "noise floor" are noise, and therefore should not be considered during normalization.

  • For samples where signal is completely "below noise" it would result in data not being normalized, which is preferable since there is no reliable signal. In this case the usual MA outlier strategy would be effective.
  • For samples with reasonable signal with slope deviating from zero, it should have no effect (no negative effect).

27jun2023

• jammaplot() and ggjammaplot() - controlSamples

• improve the indication that a sample (panel) was used as a control during data centering. Currently displays an asterisk "*" in the top-left, however it is not visible in all plots, especially when there are outlier samples. Also, there is no legend indicating the meaning of the asterisk.

• Consider using asterisk only for samples excluded during centering, therefore by default no asterisk is necessary.
• Consider using ComplexHeatmap::Legend() to create a custom legend. It would be used to display "* - samples excluded during centering" and optional highlight points.

• Consider argument to display/hide the color legend, useful when the color legend might be too large to display comfortably. Instead provide method for users to create their own legend.

• jammaplot() and ggjammaplot() - MAD factor label box

• Consider displaying the MAD factor inside a label box, to improve legibility when the text overlaps the point density. This change could be optional, controlled with a new argument.

• Consider using grid functions for drawLabels() to allow much more control over label placement, for example avoiding overlaps between subtitle and MAD factor labels by shifting one label by the height of the other label. This suggestion might affect jamba::drawLabels().

30may2023

• volcano_plot()

• method to highlight points (rows) and assign colors should be consistent with jammaplot(), with similar color legend drawn.

• consider colorized smooth scatter in panels that match the statistical thresholds used.

  • Idea is to render smooth scatter in panels, where color density is restricted to points inside these regions, then render these panels exactly at these borders. Effectively like running the plot three times (red/blue/grey) then copy/pasting only the relevant regions for use in the final plot. In fact, that could be one potential implementation strategy. It could be faster and more reliable than subsetting points, where density at the borders might be mis-calculated.
  • top-left: down-significant (blue)
  • top-right: up-significant (red)
  • top-center: no change, met significance (grey)
  • bottom-left, bottom-center, bottom-right: no statistical change (grey)

• Consider option to use scatter points instead of smooth scatter, with colorized points in each relevant region.

  • Primary driver would be for volcano plots with many relatively few points to display, the density plot would be too obscure. E.g. NanoString, SomaLogic, with 100 to 1,000 points.

25may2023

• Adjust outer margin for base plots

• display y-axis labels only on the first plot each row

• shrink the margin between plot panels

16may2023

• volcano_plot()

• allow SummarizedExperiment input

• allow optional labeling of genes
• allow optional ggplot2 output, which would make labeling genes much more feasible.

22mar2023

• Empty control group updates

• Date centering by centerGeneData() should be mirrored in MA-plots for the same situation where control samples are entirely NA, causing remaining values to become NA and therefore not be visible on MA-plot panels.

12mar2023

• centerGeneData()

• situation occurs when centering versus controlSamples results in rows where all controlSamples have NA values, thereby causing all centered values to become NA.

• goal is to offer alternatives where appropriate:

  1. "na": leave values NA (current behavior, default)
  2. "row": center versus row non-NA values
  3. "floor": center versus numeric floor
  4. "min": center versus the minimum observed value

22nov2022

• jammaplot_se() - customized jammaplot() for SummarizedExperiment input

• analogous to jamses::heatmap_se() so it should share argument style

• normgroup default uses column(s): `colData(SE)[[normgroup]]
• centerby_colname default uses column(s): `colData(SE)[[centerGroups]]
• sample_color_list optional input for colorization

28jun2022

• ggjammaplot() issues:

• bw_factor was behaving exactly opposite as expected

• COMPLETE: color gradient by ggplot2::stat_density_2d() is inconsistent between outlier and non-outlier point ranges.

• jammaplot() and ggjammaplot() may need one argument to adjust detail of density plots overall. Let it handle passing binpi and bwpi to jamba::plotSmoothScatter(), or using ggplot2 geom arguments.

31may2022

• COMPLETE: Related to indicating controlSamples below, some plot hook to add annotations to each panel while plotting for R base graphics. This feature is likely already possible with ggjammaplot() with custom ggplot2 layers.

• COMPLETE: new argument plot_hook_function allows full customization after each panel is rendered, for jammaplot() in base R graphics.

• Note: ggjammaplot() is fairly slow for this purpose, rendering may overall be slower than base R graphics, though this difference could be from lack of particular optimizations.

• Visual differences in jammaplot() and ggjammaplot() assignment of colors to point density. Unclear whether this difference is due to cropping of points outside the visual range, as happens with base R graphics plotSmoothScatter() and applyRangeCeiling=TRUE.

• ggjammaplot() does not honor the order of samples when applying facet_wrap(), it should convert the facet column to factor with levels equal to the order of columns to be plotted.

• Consider subtitle being able to use one or more colnames in colData(se) when the input data is SummarizedExperiment.

• When multiple columns are provided, include them as multiple lines, each colored using colorSub?

• Consider using shadowText() to display the MAD values, otherwise it is not visible in some panels.

26may2022

• COMPLETE: There should be some indication for samples that are controlSamples during centering.

• Perhaps an asterisk in the topleft corner inside each plot panel?

• Allow sample_color_list input as alternative to colorSub? Or auto-detect list input and try to match values in the list.

• COMPLETE: Update the usage of drawLabel() to size the title box at least the width of each plot panel.

• FIXED: volcano_plot() throwing an error:

• "Error in utils::modifyList(default_params, new_values): is.list(x) is not TRUE

• update_function_params(function_name = "volcano_plot", param_name = "color_set", new_values = color_set) at jam-volcano-plot.R#374

11may2022

• COMPLETE: jammaplot() should have some ability to provide column labels, in place of using colnames(x) which may be a super-long text string.
• jammaplot() consider using jamba::adjustAxisLabelMargins() for panel margins by default, making margins optional for custom use. This change would ensure each margin fully displays text labels, closer to how ggplot2 works.

Potential bugs:

• COMPLETE: jammaplot() highlightPch point shapes are not honored in the legend.

• COMPLETE: jammaplot() draws plot labels after highlightPoints, which can obscure the highlightPoints. Ideally, draw the labels then the highlighted points. This bug may not be evident with ggjammaplot().

• Partially completed by moving title box labels outside the plot. It is still possible with subtitle box labels, but will leave as-is for now.

• ggjammaplot() does not display subtitle box in the bottom-left. Consider using ggtext or ggplot2::geom_label().

• jammaplot() and ggjammaplot() should somehow indicate which samples were used as controlSamples. Perhaps asterisk "*" in the title?
• The MAD factor label is difficult to read when it overlaps points, particularly highlight points.
• When only one sample per centerGroups, hide MAD factor "NaN".

outlier detection in jammaplot by leave-one-out

Basic workflow:

• within each centerGroups grouping
• iterate each sample to leave one sample out
• call jammacalc() to calculate MADfactors for all replicates, focusing on the omitted sample.
• determine if there are robust sample outliers

volcano_plot()

• COMPLETE. Add new function.
• Add ggplot2 variation on this function.
• Add volcano_sestats() that takes sestats input from jamses::se_contrast_stats().

ggjammaplot()

• make empty plot panels completely blank, relevant when using blankPlotPos
• set xlab, ylab using summary, difference labels
• add subtitleBox to bottomleft corner
• investigate using element_text() instead of ggtext::element_textbox()
• allow geom_text_repel() to label highlighted points

• consider selectable x- and y-ranges, to highlight a box and points within it

• Needed a workaround to build pkgdown site, see: https://github.com/r-lib/pkgdown/issues/1157

New functions

• jammaplotDispEsts() wrapper for DESeq2::plotDispEsts(), although this function needs the newer colorized plotSmoothScatterG2().

compatibility with SummarizedExperiment

Bug fixes

• jammaplot() argument ablineV is not functioning properly.
• jammaplot() highlight legend is not using highlightPch.

Vignettes

1. Guides for MA-plots.

2. Basic guide to MA-plots for gene expression data.

3. check data normality, apply appropriate transform, normalize data

4. check within-group variability
5. highlight points

6. common patterns and what they mean:

   • shifted up/down
   • skewed up/down
   • low signal-to-noise, no signal
   • the 45-degree lines
   • batch effects
   • technical versus biological controls

7. non-parametric (rank-based) MA-plot

8. When to do use centerGroups, controlSamples.

9. How to interpret global-, group-, and technical replicate-centered data.
10. How to detect sample outliers using a MAD factor threshold.
11. How to guide data normalization by MA-plot review.

useful functions

• log2fold_to_fold() and fold_to_log2fold() - to interconvert:

• normal space fold changes, which could be represented as positive and negative values (e.g. 2-fold and -2-fold) or as ratios (e.g. 2-fold and 0.5-fold); and

• log2 fold change values
• Consider fold_sign() function that takes either as input and returns either 1 or -1, and by default never returns 0 since 1-fold change cannot easily be multiplied by its fold_sign() without causing it to become zero. More thought to be had as to the workflow.

Interface with other R packages

DESeq2

• plotMA() is used for the DESeq2::DESeqResults object, highlighting points that meet alpha < 0.1 by default.
• Add new method to run jammaplot() on the count data, optionally transformed using their recommended approach, or use useRank=TRUE.

Bug fixes

• Version 0.0.10.900 fixed a bug where rowGroupMeans() was used to center values, but used default na.rm=FALSE, which caused groups with missing values not to display a centered value for other non-NA samples. The new version should provide two options:

  1. Hide or display values where groups with n>1 members have only one non-NA value. The reasoning is that the MA-plot is intended to show "difference from mean" and has far less utility when a fraction of rows has only one non-NA value in the group, thus emphasizing the display of "zero difference" in those samples. Hiding these values therefore helps display the variability where data is available to judge the difference from mean.
  2. Hide groups with any NA values.

Refactoring ideas

• Consider using jamba::rowGroupMeans() within centerGeneData() which would allow optional outlier detection, which could substantially improve the quality of MA-plot panels.
• jammagg() or something similarly named, to produce a ggplot2 object.
• One goal for ggplot2 output is to produce interactive visualizations with plotly; however, if that is not sufficient for the desired properties, e.g. useful hover text over the smooth scatter density, then a custom interactive plot function may be needed, for example direct calls to plotly instead of using the ggplotly wrapper function.

Update to handle SummarizedExperiment objects

• centerGroups should be able to take colnames from colData(x) to define groupings.
• jammaplot.SE() could be specific to SummarizedExperiment objects. It would require the names(assays(SE)) to define the data matrix to use. It could even recognize sample groups from colData(SE), or from internal design matrix used for statistical testing.

Highlighted points

• Consider allowing highlighted points per panel, for example, showing gene hits only in the panels relevant to that comparison. However, there is a workaround, using whichSamples which will create the MA-plot data, but only display the samples of interest.

Color legend for highlighted points

• Add optional color legend at bottom of the figure labeling the colors highlighted on the plot.

Enhance the returned data

• Currently returns a list of 2-column matrices
• Return data.frame with properly labeled colnames
• Add columns:
  • indicating the centerGroups value if defined
  • whether the sample is a control sample within its centerGroup
  • highlight label, highlight point color
  • title box color

User should be able to take the returned data.frame list, and make a tall data.frame sufficient for ggplot2, or sufficient to answer the question "What is that outlier datapoint?"

Interactive plots using plotly

Future idea:

• Convert plotSmoothScatter to generate a heatmap-ready density plot for each panel.
• For each cell in the panel, optionally update the label so it lists the point label(s) represented in that cell; alternatively simply label with the number of points represented.

Accessory function to select points

• A common workflow request stems from the question "What are those points?" A wrapper function was written to allow clicking twice inside an active plot device to define a rectangle, then returning the rownames of the corresponding points.
• The steps above could be used to supply coordinates from something like R-shiny, to request the rownames of the points specified.

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