make.autograph: make.autograph - Creates plots using ggplot2

In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis

make.autograph - Creates plots using ggplot2

Description

This function allows you to generate quantitative plots of your data. Creates scatter plots. If interested in generating other plots (bar graphs) or adding statistics, we recommend reading more on using 'ggplot2' (for more info https://ggplot2.tidyverse.org/). Uses the package 'ggplot2' to generate plots, 'data.table' to manipulate data.

Usage

make.autograph(dat, x.axis, y.axis, colour.by, colours, 
y.axis.label, grp.order, title, filename, scale, dot.size, width, 
height, path)

Arguments

dat	NO DEFAULT. data.frame.
x.axis	NO DEFAULT. Character or numeric. Selects column that will specify x-axis.
y.axis	NO DEFAULT. Character or numeric. Selects column that will specify y-axis.
colour.by	DEFAULT = x.axis. Character, column name. Selects column that will determine differentiator of colour in plots.
y.axis.label	NO DEFAULT. Character. Specify y-axis label. Can be "" if one is not desired.
grp.order	DEFAULT = NULL. String of characters or numbers. Specify order of group for x-axis.
colours	DEFAULT = NULL. String of characters. Will determine the colours that will differentiate between colours specified by 'colour.by'.
my_comparisons	DEFAULT = NULL. A list containing vectors – each a pair of groups for comparison.
Variance_test	DEFAULT = NULL. Can be 'wilcox.test' (non-parametric) or 't.test' (parametric)
Pairwise_test	DEFAULT = NULL. Can be 'kruskal.test' (non-parametric) or 'anova' (parametric)
title	DEFAULT = paste0(y.axis.label, " - ", y.axis). Character. Specify title of plot on graph. Default combines 'y.axis.label' and 'y.axis'.
subtitle	DEFAULT = NULL. Plot subtitle.
filename	DEFAULT = paste0(y.axis.label, " - ", y.axis, ".pdf"). Character. Specify name plot will be exported as. Default combines 'y.axis.label' and 'y.axis'. Make sure to end with ".pdf" so file is correctly saved.
violin	DEFAULT = TRUE. Add violin plot underneath the data points.
scale	DEFAULT = "lin". Character. Select y-axis scale. Can also be "sci".
dot.size	DEFAULT = 5. Numeric. Specify size of dots on plot.
width	DEFAULT = 5. Numeric. Specify width of plot.
height	DEFAULT = 5. Numeric. Specify height of plot.
max.y	DEFAULT = 1.4. Multiplier for plot heigh – allowing room for stats.
path	DEFAULT = getwd(). The location to save plots. By default, will save to current working directory. Can be overidden.

Author(s)

Thomas M Ashhurst, [e-mail] Felix Marsh-Wakefield, [e-mail]

Examples

dat <- data.frame(Samples = c("Mock_01", "Mock_02", "Mock_03", "WNV_01", "WNV_02", "WNV_03"),
                  Group = c(rep("Mock", 3), rep("WNV", 3)),
                  Tcells = c(20, 40, 30, 60, 70, 80),
                  Bcells = c(90, 95, 70, 20, 15, 30),
                  Batch = c(1,2,1,3,2,1)
                  )

Spectre::make.autograph(dat = dat,
                        x.axis = "Group",
                        y.axis = "Tcells",
                        colour.by = "Batch",
                        colours = c("Black", "Red", "Blue"),
                        y.axis.label = "Proportion"
                        )

ImmuneDynamics/Spectre documentation built on Oct. 12, 2024, 7:55 p.m.