multibarplotsDiversityCond: For easier comparison, plot the uniquely expressed genes...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

For easier comparison, plot the uniquely expressed genes (colored by tissues) in two studies Allows to consider several thresholds of expression for the second study.

Description

For easier comparison, plot the uniquely expressed genes (colored by tissues) in two studies Allows to consider several thresholds of expression for the second study.

Usage

multibarplotsDiversityCond(DF1, DF2, threshold1 = 0, threshold2 = c(0,
  1, 5), label1 = "Proteins", midLabel1 = "(", endLabel1 = ")",
  label2 = "mRNA", midLabel2 = "(", endLabel2 = "FPKM)",
  sorted = TRUE, common = TRUE, colorpal = NULL, publish = TRUE,
  output = "count", verbose = TRUE, decreasing = TRUE, ...)

Arguments

DF1	numeric data.frame (first study expression data)
DF2	numeric data.frame (second study expression data)
threshold1	numeric. Expression above which a gene is considered as expressed for the first study
threshold2	a vector of numeric. Expression values above which a gene is considered as expressed for the second study
label1	character string. Label for the first study to use on the plot (first part) Default: 'Proteins'
midLabel1	character string. Label for the first study to use on the plot (first part before threshold) Default: '('
endLabel1	character string. Label for the first study to use on the plot (second part after threshold) Default: ')'
label2	character string. Label for the second study to use on the plot (first part) Default: 'mRNA'
midLabel2	character string. Label for the second study to use on the plot (first part before threshold) Default: '('
endLabel2	character string. Label for the second study to use on the plot (second part after threshold) Default: 'FPKM)'
sorted	boolean. Default: TRUE. Whether the tissues should be sorted in function of their number of tissue specific genes
common	boolean. Default: TRUE. Whether the two studies should share identical rownames and colnames
colorpal	colour palette to use in the figure (done with ggplot2::scale_fill_manual)
publish	boolean. Default: TRUE. Whether to apply ggplot2::theme_bw to the plot.
output	character string. Switch that allows to choose between 'count' for the count of unique genes across the tissues or a ratio based on the distribution of the tissue specific genes across each study.
verbose	boolean. Default: TRUE.
decreasing	boolean. Default: TRUE. Whether the sorting should be done in decreasing order.
...	other arguments that can be used by ggplot2::theme_bw()

Value

a list of object that would allow to create a figure

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.