createPlotlist: Function to create descriptive plots of spot localization per...
In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data

createPlotList

R Documentation

Function to create descriptive plots of spot localization per group of cells

Description

createPlotList() is a plotting function which combines detected fluorescent spot localization with mesh outline information to plot demographs, projections, histograms and a data summary in one go. These functions are all combined because they need similar data preparation. The idea is that after using this function, you have a good overview of the localization of your protein inside the cells. Sometimes this analysis can be enough to show where a protein localizes, but in other cases (when proteins are very mobile or localize heterogeneously, for instance), this may rather serve as a starting point for more detailed analysis. Therefore, the data generated to make these plots is also returned by the function.

Usage

createPlotList(spotdata,
               meshdata,
               groups=4,
               colorpalette="GreenYellow",
               lineColor="white",
               mag="No_PixelCorrection",
               AllPlot=F,
               Xm="X",
               Ym="Y",
               viridis=FALSE,
               showPlot=TRUE,
               getData=FALSE,
               getSummary=TRUE)

Arguments

`spotdata`	Data frame containing -at least- column with spot x-localizations, y-localizations and frame number. When the variable meshdata is not given, additional required columns are cell ID, relative x-localization ("l" or "Lmid") and relative y-localization ("d" or "Dum").
`meshdata`	Data frame containing -at least- the x and y coordinates of the cell meshes, the maximum cell width, maximum cell length, cell ID and frame. Optional.
`groups`	Number of groups the data will be divided in. Default = 4.
`colorpalette`	Color palette the heatmap plots will be plotted in. Default is "GreenYellow". Check which palettes are loaded by `showColorPaletes()` and add your own palette using `addPallete()`
`lineColor`	to be able to change the outlines of the cell and pole localizations in demographs, set lineColor. Default is "white".
`mag`	The name of the conversion factor for pixel to micrometer. Default is "No_PixelCorrection" which is 1. Check `getPixels2um` for the loaded conversionfactors and use `addPixels2um("ConversionName", conversionfactor)` to add a conversion factor to the list.
`AllPlot`	When `TRUE`, the output x/y plots will have sideplots with histograms of the spot localization. When `FALSE`, only the x/y plots will be plotted.
`Xm`	By default, the column names of the x/y coordinates in the MESH data frames are "X" and "Y". When this is not the case, one can tell the function by using `Xm` and `Ym`. Enter a character string with the name of the x-coordinate column for Xm, and the name of the y-coordinate column for Ym.
`Ym`	See Xm
`viridis`	when `viridis==TRUE`, the `colorpalette` needs to be one of the `viridis` color palettes ("A", "B", "C", "D", "E", "magma", "cividis", "viridis", "plasma" or "inferno")
`showPlot`	when `showPlot==TRUE`, a menu will be shown after the function is finished, which enables the user to view the plot output of the function.
`getData`	when `getData==TRUE`, the output list will include the input dataframes `spotdata` and (if given) `meshdata`, which include the quantile classification and the relative localization of the spots.
`getSummary`	when `getSummary==TRUE`, the output list will include the `data_summary` (see below).

Value

A list consisting of the following items:

`$lengthplot`	Heatmap histogram plot of the length-axis localizations of the spots ordered by the length of the cell.
`$widthplot`	Heatmap histogram plot of the width-axis localizations of the spots ordered by the length of the cell.
`$qplots_separate`	If the outlines of the cell are not added to the function (dataframe `MESH` not indicated), the output will be a list of plots of length `inp`, with relative x/y coordinates of the spots plotted as a density function. The data is grouped by the variable `bycol`, which is `length` by default.If the outlines of the cells are added to the function (dataframe `MESH` indicated), the average cell outline of each group will be overlayed on top of each plot. If `AllPlot==TRUE`, histograms of the x and y coordinates of the spots will be added as sideplots.
`$qplots`	for easy use, qplots is a `grob` arrangement of the group-plots `qplots_separate`: using `plot()` you can immediately view them in the Rstudio plots window.
`$plottotal`	Relative x/y coordinates of all spots with average cell outline overlayed. If `AllPlot==TRUE`, the x/y coordinates will be plotted as histograms on the x and y axis of the plot.
`$histograms`	1D density plots of the spot localization on the length axis of the cells, grouped by `bycol` in the amount of groups defined by `groups`.
`$spotdata`	data frame containing the groups, relative x/y localizations of the spots and cell length/width
`$meshdata`	if `MESH` is included, the function returns a dataframe including the rotated meshes and groups.
`$data_summary`	a character vector, or when `groups>1`, a list of character vectors summarizing the most important data features of each size group and the full dataset.

Note

This function is meant to give an overview of the data. Check the tutorials on the wiki page for examples of modifying individual plots.

Author(s)

Renske van Raaphorst

References

These plotting functions were developed for:

van Raaphorst, Renske, Morten Kjos, and Jan-Willem Veening. "Chromosome segregation drives division site selection in Streptococcus pneumoniae." Proceedings of the National Academy of Sciences 114.29 (2017): E5959-E5968.

Examples


## Not run: 
##use data from example dataset

##download example datasets DnaX_tracks.rda & DnaX_mesh.rda
##from https://veeninglab.com/f/example_datasets.zip

load("DnaX_tracks.rda")
load("DnaX_mesh.rda")

##create list of plots, ordered by length, grouped in 6 groups.
GFPlist <- createPlotList(DnaX_tracks, DnaX_mesh, groups=6, colorpalette="GreenYellow", AllPlot=T)

#have a look at the "plottotal" plot
plot(GFPlist$plottotal)

#save PDF of the 6 grouped plots (qplots)
ggplot2::ggsave(GFPlist$qplots, filename="GroupPlots.PDF")

#see summary:
GFPlist$data_summary

## End(Not run)

vrrenske/shinyspots documentation built on Oct. 28, 2023, 12:26 p.m.