Description Usage Arguments Value Examples
View source: R/multiple_signatures_plot.R
This function generates a plot of the member genes of a given gene set across multiple signatures. Its first intention is to illustrate the so called 'percent rank' of a given gene from a given gene set.
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sigmat |
gene expression matrix, usually of raw values such as read counts, TPM or FPKM |
geneset |
a character vector representing one gene set |
color |
single character string indicating a color for the bar lines |
signatureNames |
Character vector of length 2, specifying the extremes of the signature |
gs_label |
single character string to label the gene set under investigation |
column_col |
vector of color ids (character, hex, etc) that must match the number of columns in the signature matrix. |
relative_sigs |
logical, whether signatures are considered relative, e.g. t-stats or logFC. Will carry out fgsea. |
aREA_scores |
numeric vector that must match the number of columns from signature matrix, alternative to average rank metric |
... |
given for compatibility, particularly for the adjustment of cex for various text labels |
scale_alpha |
logical, whether to scale alpha values for bars, defaults to TRUE |
Nothing, a plot is generated in the default output device
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