barplot_data: Generate barplots

In MACSQuantifyR: Fast treatment of MACSQuantify FACS data

Description

Uses the informations stored in the statistic tables of the MACSQuant object to generate barplots for the specified conditions. Plots can also be saved in the form of a png file in the output_MQ directory.

Usage

barplot_data(MACSQuant,plt.col=NULL,plt.conditions=NULL, plt.flavour=NULL,
plt.labels = NULL, plt.combo=FALSE,plt.3D.only = NULL,...)

Arguments

MACSQuant	object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table
plt.col	In case of manual run is used to define the bar colors. (must be the same for all conditions)
plt.conditions	user defined vector of conditions to plot (example: plt.conditions=c(1:9))
plt.flavour	Which barplot to produce, cell count or percentage of fluorochrome (i.e: "counts","percent")
plt.labels	xlabels of the plot
plt.combo	Does the experiment involves multiple variables (i.e some condition are a drug combination screening)
plt.3D.only	Whether to plot 3D barplot alone
...	params for lattice cloud namely z and x for parameter screen default for z and x are c(-110,-70) and argument xlab and ylab

Value

returns a barplot of the data

Examples

drugs_R_image <- system.file("extdata",
    "drugs.RDS",
    package = "MACSQuantifyR")
MACSQuant <- readRDS(drugs_R_image)
flavour <- "counts"
number_of_conditions <-
    slot(MACSQuant, "param.experiment")$number_of_conditions
plt.col <- c(rep(2, number_of_conditions), 1)
barplot_data(MACSQuant,
    plt.col = plt.col,
    plt.conditions = NULL,
    plt.flavour = flavour,
    plt.labels = NULL,
    plt.combo = FALSE)

MACSQuantifyR documentation built on Nov. 8, 2020, 5:08 p.m.