build.heatmaps: Build heatmaps
In JonathanIrish/MEMv3: Marker Enrichment Modeling (MEM)

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/build_heatmaps.R

Takes matrix list generated from MEM as input and outputs MEM labels, heatmap of population median values, and heatmap of MEM scores.

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    build.heatmaps(exp_data, cluster.MEM = "none", cluster.medians = "none", 
    cluster.IQRs = "none", newWindow.heatmaps=FALSE, display.thresh = 0, 
    output.files = FALSE, labels = FALSE, only.MEMheatmap = FALSE)

`exp_data`	List of matrices generated as output from `MEM aka MEM_values`
`cluster.MEM`	`"none"`,`"row"`,`"col"`,or `"both"`; which dimension(s) of the MEM heatmap to hierarchically cluster. See `Details` for more information.
`cluster.medians`	`"none"`,`"row"`,`"col"`,or `"both"`; which dimension(s) of the median heatmap to cluster. If `"none"`, the median row and column order will match order of the MEM heatmap.
`cluster.IQRs`	`"none"`,`"row"`,`"col"`,or `"both"`; which dimension(s) of the IQR heatmap to cluster. If `"none"`, the IQR row and column order will match order of the MEM heatmap.
`display.thresh`	Numeric; 0-10. Markers with enrichment scores that are equal to or greater than `display.thresh` will be displayed as row names on `MEM heatmap`.
`newWindow.heatmaps`	`TRUE` or `FALSE`; whether or not to pop out new windows to display the MEM, median, and IQR heatmaps
`output.files`	`TRUE` or `FALSE`; If `TRUE`, output of `build.heatmaps` will be written to folder `output folder` that is created as a subdirectory of the working directory. Written files include txt file containing MEM labels (row names), and txt files containing MEM scores, medians, and IQR values.
`labels`	`TRUE` or `FALSE`; whether or not to include MEM labels in the MEM heatmap
`only.MEMheatmap`	`TRUE` or `FALSE`; whether to only show MEM heatmap or all relevant heatmaps (MEM, median, IQR)

Heatmaps are clustered using the default complete linkage hierarchical clustering in the hclust function. See heatmap.2 and hclust for more information.

Heatmaps of median, IQR, and MEM values on each population; optionally written to file. X11 is used to open plots in a new window. When windows open, user must click within the window to permit R to print the heatmap to that window (the window will remain blank until user clicks on it).

Kirsten Diggins, Sierra Barone, Jonathan Irish

Diggins et al., Nature Methods, 2017

MEM, heatmap.2, hclust

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

build.heatmaps(MEM_values, cluster.MEM = "both", cluster.medians = "none", 
    cluster.IQRs = "none", newWindow.heatmaps=FALSE, display.thresh = 1, 
    output.files = TRUE, labels = FALSE, only.MEMheatmap = FALSE)