plot_bar_list: Plot frequencies in a barplot (use in combination with...
In tkostas/komics: Tools to analyze omics data

Description Usage Arguments Value Examples

Reads a list of frequencies calculated for different groups (see above_threshold) and makes a barplot for the mean between groups or for the individual measurements. Use to plot number of identified peptides/proteins per group or per sample.

1	plot_bar_list(x, compare = "groups", ylim = c(0, NA))

`x`	Input list. Each element of the list has a title that will be used to define the group and to order the bars in the bar-graph. Every element of this list is a vector containing numeric values (e.g. number of proteins per experiment). The names of this vector are the experiments. Use as input the output of the above_threshold function.
`compare`	Character vector that can be "groups" or "experiments", either to summarize values for groups or show the values for individual experiments. If "groups" are selected, the mean value +- SEM is plotted.
`ylim`	Numeric vector, defining min and max value for the y axis.

Returns a graph.

# first calculate the frequencies using the above_threshold function
place the group names in the correct order before calculating frequencies
Bmp4 <- "Bmp4"
Ctrl <- "Ctrl"
group_ids <- list(Bmp4 = Bmp4,
                  Ctrl = Ctrl)

number_of_ids <- above_threshold(data, group_ids = group_ids, threshold = 0)

# use the list with frequencies as input to make the barplots

# summarize identifications per 'group'
plot_bar_list(number_of_ids, "groups")

# plot frequencies per 'experiment'
plot_bar_list(number_of_ids, "experiments")