plot_mir_count_threshold {miRetrieve}

Plot occurrence count of miRNA names over different thresholds

Description

Plot occurrence count of distinct miRNA names over different thresholds.

Usage

plot_mir_count_threshold(
  df,
  start = 1,
  end = 5,
  bins = NULL,
  colour = "steelblue3",
  col.mir = miRNA,
  col.pmid = PMID,
  title = NULL
)

Arguments

df

Data frame containing columns with miRNAs and PubMed-IDs.

start

Integer or float. Must be greater than 0 and smaller than end.

end

Integer or float. Must be greater than 0 and greater than start. If start >= 1, plot_mir_count_threshold() plots number of miRNAs above different absolute thresholds, ranging from start to end. If start >= 0 and end <= 1, bins must be specified. If bins is not specified, bins is automatically set to 10. plot_mir_count_threshold() then plots number of miRNAs above different thresholds, ranging from start to end in n bins. If start >= 0 and end <= 1 and the value of start is too low for the number of miRNAs to be plotted, plot_mir_count_threshold() raises a warning, suggesting a more appropriate start value.

bins

Integer. Optional. Only necessary if start >=0 and end <=1. Specifies number of bins between start and end. If start >= 0, end <= 1, and bins is not specified, bins is automatically set to 10.

colour

String. Colour of bar plot.

col.mir

Symbol. Column containing miRNAs.

col.pmid

Symbol. Column containing PubMed-IDs.

title

String. Plot title.

Details

Plot occurrence of distinct miRNA names over different thresholds. These thresholds can either be absolute values or floating values between 0 and 1. If the thresholds are absolute values, number of distinct miRNA names mentioned in at least n abstracts are plotted, where n is the range of thresholds defined by start and end. If the thresholds are floating values, bins must be specified as well. Then the umber of distinct miRNA names mentioned in at least n abstracts over bins are plotted, where n is the range of thresholds between start and end. Overall, plotting can help in identifying if the abstracts at hand mention different miRNAs in a balanced way, or if there are few miRNAs dominating the field.

Value

Bar plot counting the occurrence of miRNA names above different thresholds.

See Also

count_mir_threshold(), count_mir(), plot_mir_count()

Other count functions: count_mir_threshold(), count_mir(), count_snp(), plot_mir_count()