barplot_data {MACSQuantifyR} | R Documentation |
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.
barplot_data(MACSQuant,plt.col=NULL,plt.conditions=NULL, plt.flavour=NULL, plt.labels = NULL, plt.combo=FALSE,plt.3D.only = NULL,...)
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 |
returns a barplot of the data
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)