OmicInt (version 1.1.7)

pattern_plots: pattern_plots

Description

pattern_plots function uses a subsetted pattern data from the function pattern_search. The function plots distribution plots as well as a selected set of genes and how they changed patterns. NOTE: if there are too many genes (>300), then individual gene expression plots will not be full because there is not enough colours in a palette to depict them all; in such a case, the function's violin plot can be used to assess the overall distribution and then the function should be repeated for filtered gene sets of interest to inspect individual expression values for each gene.

Usage

pattern_plots(data, meta, low = NA, high = NA, Condition = "Condition_1")

Arguments

data

Requires a data frame of normalised scores subsetted from pattern_search function. Class - string

meta

Requires a path variable to a data frame of metadata in CSV format. Class - string

low

the lowest value for the expression value; class - integer or float

high

the highest value for the expression value; class -integer or float

Condition

Requires a condition name to select if there are multiple conditions in meta data file, default "Condition_1". Conditions need to match between pattern_search and pattern_plot functions.Class - string

Value

function plots multiple plots, class - plots

Examples

# NOT RUN {
path_to_test_data<- system.file("extdata","subsetted_data.csv", package="OmicInt")
path_to_meta_data<- system.file("extdata", "meta_data.csv", package="OmicInt")
# basic usage of pattern_search
pattern_plots(path_to_test_data,path_to_meta_data, 20, 10000)
# }