plot_sedesign: Plot sedesign object contrasts

In jmw86069/jamses: Jam SummarizedExperiment Stats

Plot sedesign object contrasts

Description

Plot contrasts from sedesign object (in development), showing one-way contrasts as block arrow, and two-way contrasts as two block arrows connected in proper order.

Usage

plot_sedesign(
  sedesign,
  se = NULL,
  factor_names = NULL,
  factor_sep = "_",
  contrast_sep = "-",
  axis1 = NULL,
  axis2 = NULL,
  axis3 = NULL,
  axis4 = NULL,
  which_contrasts = NULL,
  contrast_style = c("comp", "contrast", "none"),
  contrast_labels = NULL,
  oneway_position = 0.9,
  twoway_position = 0.5,
  contrast_position = NULL,
  contrast_depths = NULL,
  sestats = NULL,
  sestats_style = c("label", "number", "simple label"),
  assay_names = NULL,
  cutoff_names = NULL,
  label_cex = 1,
  arrow_ex = NULL,
  flip_twoway = FALSE,
  colorset = NULL,
  twoway_lwd = 5,
  extend_ex = 0.5,
  extend_angle = 10,
  bump_factor = 1,
  group_buffer = 0.02,
  group_border = "grey65",
  group_fill = "grey95",
  replicate_color = "grey40",
  replicate_cex = 0.8,
  do_plot = TRUE,
  plot_margins = c(0.1, 0.1, 0.1, 0.1),
  plot_type = c("base", "grid"),
  verbose = FALSE,
  debug = FALSE,
  ...
)

Arguments

sedesign	SEDesign object as returned by groups_to_sedesign().
se	SummarizedExperiment (optional) and not yet used by this function. In future this object may be used to assign factor level order to factor values.
factor_names	character vector equal to the number of delimited values in each group name, recognized in the group names of the design matrix of sedesign as in colnames(sedesign@design).
factor_sep	character string separator between factor values in each group name, typically factor_sep="_".
contrast_sep	character string separator between group names in each contrast name, typically contrast_sep="-".
axis1, axis2, axis3, axis4	character vectors which define the factors to represent on each axis, with axes defined in order 1=bottom, 2=left, 3=top, 4=right. All factors in factor_names must be represented.
which_contrasts	one of the following: numeric index of contrasts defined in sedesign, or character vector of values present in contrast_names(sedesign). When a two-way contrast is defined, its component one-way contrasts are also included.
contrast_style	character string deciding how to format the contrast: "comp": calls contrast2comp() "contrast": uses the contrast as-is "none": hides the contrast label, appending contrast_labels when provided
contrast_labels	character vector of labels named by contrast
oneway_position, twoway_position	numeric value between 0 and 1, which define the default position of each contrast label for one-way and two-way contrasts, respectively. These values are overridden by optional argument contrast_position when supplied. 0 places the label toward the beginning of the arrow, which also applies right/top justification of text at the start of the arrow. 1 places the label at the end of the arrow, which also applies left/bottom justification of text at the end of the arrow.
contrast_position	numeric vector named by contrast, whose values position each contrast label given. Default values are defined by oneway_position and twoway_position, except where defined by contrast_position.
contrast_depths	numeric with one or more values used to display only contrasts of the given depth: 1=oneway, 2=twoway. When NULL all contrasts are displayed.
sestats	list object that contains element "hit_array" as produced by se_contrast_stats(), with statistical hits for each contrast, after applying statistical cutoffs. When supplied, statistical hits are included in each contrast label. The three relevant optional values used to specify specific hits: "assay_name": this argument defines the values from SummarizedExperiment::assays() that were used in the contrasts. "cutoff_name": this argument defines a specific cutoff to use, otherwise hits from any applied cutoff are included. "contrast_name": this value uses argument which_contrasts
sestats_style	character string indicating how to present the number of hits for each contrast. "label": uses the full label: number hits (number up, number down)" "number": uses only the number of hits "number" "simple label": uses a simple label: "number hits" without the number of hits up and down.
assay_names, cutoff_names	character values used with sestats to define the statistical hits to use when sestats is supplied.
label_cex	numeric expansion factor to adjust contrast label font sizes.
arrow_ex	numeric (default NULL) to adjust arrow width and arrow head size together. When NULL it is adjusted starting at arrow_ex=1 and reduced proportional to the number of contrast bumps (parallel contrasts that would otherwise overlap). When provided as a numeric value, it is used without adjustment
flip_twoway	logical indicating whether to flip the orientation of two-way contrasts, for example "(A-B)-(C-D)" would be flipped to equivalent form "(A-C)-(B-D)", which will alter the orientation of the two-way contrast connection. Note that the individual one-way contrasts will be added if they did not already exist in the data.
colorset	character vector of colors used for one-way contrasts. When the vector contains names, they are assigned to contrast_names(sedesign), and any missing colors are assigned using colorjam::group2colors(). When the vector does not contain names, it is recycled to the number of contrast names.
twoway_lwd	numeric line width for two-way contrasts, passed to draw_twoway_contrast().
extend_ex	numeric expansion factor to define control points for two-way contrasts, beyond each one-way contrast by this fraction of the group width in the diagram.
extend_angle	numeric angle in degrees to define control points for two-way contrasts, using this angle from the end of each one-way contrast toward the other one-way contrast in the set. When the control point crosses the midpoint between the two contrasts, half the angle is used to re-define control points. When the control point crosses the other contrast in the set, the first control point is retained, and the second control point uses the opposite angle so the resulting bezier curve from the first contrast "loops around" the far side of the second contrast, then connects from the opposite side.
bump_factor	numeric factor applied to the relative amount of "bump" used to adjust contrasts which would otherwise overlap on the same x- or y-axis intercept. It can optionally accept two values, applied to the y-axis, then x-axis bump. Values range from 0 (no bump) to 1.5 (expands to full width of each group), with default 1 covering roughly 80% the size of each group box. This value is also adjusted by group_buffer.
group_buffer	numeric value (default 0.02) indicating the relative buffer in between each group square, as a fraction of total width. The range is restricted to minimum 0 (no buffer) to 0.5 (groups are drawn as a point) with recommended values between 0 and 0.1,
group_border, group_fill	character color used for the border and fill colors, respectively, to draw a square for each experimental group defined in sedesign. These values can be supplied as a named vector, whose names match the group names defined in sedesign, and they will be applied to each group. Any missing groups will used recycled values.
replicate_color	character string with R color, used for the label in each group for the number of replicates as defined in sedesign.
replicate_cex	numeric expansion factor used to adjust the font size for the replicate label in each group defined by sedesign.
do_plot	logical indicating whether to render the plot, or when do_plot=FALSE only the underlying data is returned.
plot_margins	numeric value applied to par("mar") around the plot, to define minimal whitespace around the plot.
plot_type	character string (experimental) to define one of multiple plot output types: "base" uses base R graphics. "grid" (not yet implemented) uses R grid graphics. This option is expected to enable more methods to reduce overlapping labels, and potentially labels with markdown markup.
verbose	logical indicating whether to print verbose output.
debug	logical indicating whether to print very detailed debug output.
...	additional arguments are ignored.
contrast	character contrast name

Details

TODO:

• Mostly done: Confirm functionality with different combinations of axis values.

• Confirm functionality with only one factor on one axis.

• Adjust drawing order:

  • Group contrasts into sets of two-way contrasts which share any one one-way contrast with each other. This group should be drawn together as a set, to minimize weird effects of overlaps.

  • Do not draw a one-way contrast independently when it is already being rendered as part of a two-way contrast.

• Implement method to assign colors to contrasts.

  • Simplest option: Allow color_sub whose names match values in contrast_names(sedesign).

  • Next potential option: Use color_sub to match each group name, then define either solid color from colorjam::blend_colors(), or using a color gradient for each one-way block arrow.

  • Two-way connectors use the first contrast end color, and second contrast start color as a gradient.

  • If colors are not defined per group, call design2colors()?

• DONE. Confirm/implement method to display fewer factors on axes than are present in the underlying group labels.

• Improve location of axis labels - currently uses jamba::groupedAxis() however they appear too distant from the figure itself.

• Determine method to "recognize" factor order from colData(se).

  • Simplest option is to use argument factor_names to match colnames(colData(se)) (when supplied) and use that to define factor order.

  • One option is to update group_to_sedesign() so it stores the factor design data as a data.frame with proper factor level order. This update could also benefit platjam::design2colors() by informing the necessary colData() colnames to use.

  • A simpler option is to update sedesign to include colnames(colData(se)) as a character vector, without having to store the full data.frame. It would requiring passing both the sedesign and se objects together.

  • Another option is to require colnames(colData(se)) to match the order in the group names defined in colnames(sedesign@design).

• DONE. implement block arrows functions for improved quality output.

• consider grid graphics (package vwline) or ggplot2 output.

• implement sensible method to display a subset of one-way or two-way contrasts. For example, two-way contrasts are easier to see when showing only a subset, perhaps only along one common axis.

• Consider implementing gradient colors for block arrows.

  • This enhancement requires changing block arrow from one polygon to a list of polygons, so each smaller polygon has its own color from the color gradient.

• Two-way contrasts:

  • Handle two-way contrasts for which the one-way contrasts may not also be defined.

  • Change drawing order so the one-way block arrow label is not overdrawn by the two-way connector.

    • This step probably requires grouping one-way and two-way contrasts so that for each two-way contrast, each one-way contrast is drawn, then the two-way connector, then the one-way labels.

    • Probably need helper function draw_twoway_contrast() which calls draw_oneway_contrast(), draw_twoway_connector(), and draw_oneway_label(). The one-way steps can be "skipped".

    • To be "fancy", when a one-way contrast would be rendered multiple times, the rendering should be "skipped" and rendered only the last time, so the label would always be rendered after the incoming two-way connector, and so the one-way contrast (and its label) would only need to be rendered once overall.

Value

invisible list of data.frame representing individual contrasts to be rendered. Mainly useful for reviewing the data used to produce the figure.

See Also

Other jam experiment design: check_sedesign(), contrast_colors_by_group(), contrasts_to_factors(), filter_contrast_names(), groups_to_sedesign(), sedesign_to_factors()

Examples

isamples_1 <- paste0(
   rep(c("DMSO", "Etop", "DMSO", "Etop"), each=6),
   "_",
   rep(c("NF", "Flag"), each=12),
   "_",
   rep(c("WT", "KO", "WT", "KO", "WT", "D955N", "WT", "D955N"), each=3),
   "_",
   LETTERS[1:3])
# simple data.frame with group information
idf <- data.frame(jamba::rbindList(strsplit(isamples_1, "_")))[,1:3]
rownames(idf) <- isamples_1;
# convert to sedesign
sedesign_1 <- groups_to_sedesign(idf)

# plot the contrasts
plot_sedesign(sedesign_1)

# re-order the factors along each axis
plot_sedesign(sedesign_1, axis1=1, axis2=3, axis3=2)

# flip the group ordering for two-way contrasts
# (These are mathematically equivalent, but shown in flipped orientation)
plot_sedesign(sedesign_1, axis1=1, axis2=3, axis3=2, flip_twoway=TRUE)

# plot only the two-way contrasts
is_twoway <- grepl("[(]", contrast_names(sedesign_1))
plot_sedesign(sedesign_1, which_contrasts=which(is_twoway),
   axis1=1, axis2=3, axis3=2)

group_names <- paste0(
   rep(c("DMSO", "Etop"), each=4),
   "_",
   rep(c("NF", "Flag"), each=2),
   "_",
   rep(c("WT", "KO"), 4))
sedesign <- groups_to_sedesign(group_names)
plot_sedesign(sedesign)

# plot only the two-way contrasts
is_twoway <- grepl("[(]", contrast_names(sedesign))
plot_sedesign(sedesign, which_contrasts=which(is_twoway),
   axis1=1, axis2=3, axis3=2)

jmw86069/jamses documentation built on May 31, 2024, 1:36 p.m.