multi_heat | R Documentation |
Plot one heatmap per comparison with ezheat
, where features in object
are reordered per comparison
using tab
.
multi_heat(
tab,
object,
pheno.df = NULL,
labrows = rownames(object),
labcols = colnames(object),
main = "Log2 Expression",
name = "heats",
sc = "ctr",
clip = NA,
color.v = NULL,
unique.rows = FALSE,
only.labrows = FALSE,
ntop = 50,
stat.tab = NULL,
cutoff = 0.05,
reorder_rows = TRUE,
reorder_cols = FALSE,
fontsize_row = 10,
fontsize_col = 10,
na.lab = c("---", ""),
plot = TRUE,
width = 7,
height = 7,
verbose = FALSE
)
tab |
Table of output from |
object |
Matrix-like object with features (e.g. genes) as rows and samples as columns. |
pheno.df |
Data frame with rows as samples and columns as phenotypes. |
labrows |
Labels for rows, e.g. gene symbols. This can be of length 1 (in which case it is recycled),
of length |
labcols |
Labels for columns. This can be of length 1 (in which case it is recycled),
of length |
main |
Main title of plot. |
name |
Name of file to create. Set to |
sc |
Row scaling. Should rows be centered ('ctr'), z-scored ('z'), or neither ('none'). |
clip |
Values with magnitude > |
color.v |
Color palette for heatmap. If |
unique.rows |
Logical; remove duplicated row labels to make rows unique? |
only.labrows |
Logical; only include rows where |
ntop |
Scalar number of rows to include. |
stat.tab |
Matrix-like object with statistics, such as p-values, per column, used to add "*". If given, its
dimensions should match |
cutoff |
Cutoff such that elements with |
reorder_rows |
Logical; should rows be reordered with hierarchical clustering? |
reorder_cols |
Logical; should columns be reordered with hierarchical clustering? |
fontsize_row |
Font size for row labels. |
fontsize_col |
Font size for column labels. |
na.lab |
Character vector of labels in |
plot |
Logical; should plot be generated? |
width |
Manual option for determining the output file width in inches. |
height |
Manual option for determining the output file height in inches. |
verbose |
Logical; print pruning messages to console? |
rownames(tab)
and rownames(object)
should overlap, labrows
should correspond to object
and some colnames(tab)
should end in .p
, so they can be identified.
To prevent this function from being called with an unnamed labrows
that corresponds to tab
instead of object
,
which is incorrect, if labrows
is not names(object)
(the default) then it must be named.
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