barplot_data: Generate barplots

Description Usage Arguments Value Examples

View source: R/barplot_data.R

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

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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

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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.