Skip to contents

GGplot template for other routines

ggplot_template.Rd

This routine is used by multiple others (`traitSolos`, `traitPairs`, `traitTimes`), providing one place for specialized plotting code to avoid duplication and improve visualization. However, it has some quirks to meet all needs. See details.

Usage

ggplot_template(object, ..., drop_xlab = FALSE, legend_position = "bottom")

Arguments

object

list of data frames to be plotted

...

additional parameters

drop_xlab

drop `xlab` except last if `TRUE`

legend_position

show legend if `TRUE`

facet_strain

facet by strain if `TRUE`

shape_sex

use different shape by sex if `TRUE`

boxplot

overlay boxplot if `TRUE`

Value

object of class ggplot

Details

The template consists of a wrapper (`ggplot_template`) to make multiple calls to create individual ggplot objects (`ggplot_onerow`). The `object` is a list constructed by other routines (`ggpot_traitSolos`, `ggplot_traitPairs`, `ggplot_traitTimes`) in distinct ways. Signals are passed in subtle ways about how the routines are adapted for distinct uses:

  • shape_sexdifferent shapes by `sex` if `TRUE` (all)

  • facet_strainfacet by `strain` if `TRUE` (Solos, Pairs); used in tricky ways for Times

  • legend_position"none" (Solos, Pairs) or "bottom" (Times)

  • drop_xlabdrop xlab from all but last ggplot object (Solos, Times)

  • parallel_lines

Other peculiarities are more deeply embedded in attributes either to the `object` or to the elements of the list in `object.`

  • traitnamestrait names as `dataset: trait` (`object` for all)

  • response"value","cellmean","signal" (Solos,Pairs)

  • smooth_method"lm" (Solos,Pairs), "loess" (timetype == "strain"; Times), "line" (timetype == "stats"; Times)

  • pairpair of traits (Pairs), "time" and trait name (Times)

  • sepseparator " ON " (Pairs)

  • timetype"strain","stats" (Times)

  • time"minute","week" (timetype == "strain") or "minute_summary","week_summary" (timetype == "stats") (Times)

In addition the presence or absence of a column for "condition" affects whether faceting or coloring is based on "sex" or "sex_condition". Typically, parameter `facet_strain` controls facet vs color: if `TRUE`, facet by `strain` and color by `sex` and `condition`; if `FALSE` facet by `sex` and `condition` and color by `strain`; however, if a Times plot with `response` == "value", then color by `strain`.