cmapHeatmap: Function to create an annotated heatmap of gene scores
In gCMAPWeb: A web interface for gene-set enrichment analyses

Description Usage Arguments Value Author(s)

This function takes a numerical matrix (with samples in columns and genes in rows), preprocesses the data (if desired), determines the optimal height for the heatmap and calls the .ImagePlot function to create the final heatmap figure.

cmapHeatmap(x, reference.name, col.anno = NULL, row.anno = NULL,
  file.name = "heatmap", url.base = NULL, main = "Query gene scores",
  ColorRamp = colorRampPalette(c("#044381FF", "grey95", "grey95",
  "firebrick"))(100), col.col = c(down = "black", up = "grey"),
  row.col = c(correlated = "#1B9E77", anticorrelated = "#044381FF", over =
  "#1B9E77", under = "#044381FF"), order.by.score = TRUE,
  cluster.rows = TRUE, score.cap = c(-5, 5),
  ylab = "Significant datasets")

`x`	numerical matrix with samples in rows and genes in columns.
`reference.name`	character, names of the reference cmap, used to construct the html image reference
`col.anno`	character vector with column annotations to be displayed as (horizontal) annotation bar above the heatmap. If not NULL, must contain one elment for each column of 'x'.
`row.anno`	character vector with row annotations to be displayed as (vertical) annotation to the right of the heatmap. If not NULL, must contain one element for each row of 'x'.
`file.name`	character, the path and filename (without suffix) to save the png file to
`url.base`	character, prefix for the html image reference
`main`	Character, main title of the plot
`ColorRamp`	vector of colors used for the heatmap, e.g. generated by a call to colorRampPalette
`col.col`	named vector with a color for each level of col.anno (e.g. c(up="firebrick", down="blue"))
`row.col`	named vector with a color for each level of row.anno (e.g. c(correlated="firebrick",anticorrelated="#044381FF"))
`order.by.score`	logical, should gene scores be reordered independently for each sample ?
`cluster.rows`	logical, perform hierarchical clustering on significant gene sets ?
`score.cap`	numerical vector of length two, specifying the limits of the color scale. Scores > max( score.cap) or < min(score.cap) will be set to score.cap. Default: c(-5,5)
`ylab`	character, y-axis label

list with two elements, 1. image.html: a character string with html code with the image tag refering to the output png 2. row.order: integer vector with thw row.order obtained after hierarchical clustering or NULL if no clustering was performed

Thomas Sandmann

gCMAPWeb documentation built on April 28, 2020, 8:23 p.m.