plotHM | R Documentation |
Makes heat maps
plotHM(
df,
id,
col_select,
col_order,
col_benchmark,
label_scheme_sub,
filepath,
filename,
scale_log2r,
complete_cases,
annot_cols = NULL,
annot_colnames = NULL,
annot_rows = annot_rows,
xmin = -1,
xmax = 1,
xmargin = 0.1,
p_dist_rows = 2,
p_dist_cols = 2,
hc_method_rows = "complete",
hc_method_cols = "complete",
x = NULL,
p = NULL,
method = NULL,
diag = NULL,
upper = NULL,
annotation_col = NULL,
annotation_row = NULL,
clustering_method = NULL,
rm_allna = TRUE,
...
)
df |
The name of a primary data file. By default, it will be determined
automatically after matching the types of data and analysis with an
|
id |
Character string; one of |
col_select |
Character string to a column key in |
col_order |
Character string to a column key in |
col_benchmark |
Not used. |
label_scheme_sub |
A data frame. Subset entries from |
filepath |
A file path to output results. By default, it will be
determined automatically by the name of the calling function and the value
of |
filename |
A representative file name to outputs. By default, the
name(s) will be determined automatically. For text files, a typical file
extension is |
scale_log2r |
Logical; if TRUE, adjusts |
complete_cases |
Logical; if TRUE, only cases that are complete with no missing values will be used. The default is FALSE. |
annot_cols |
A character vector of column keys in |
annot_colnames |
A character vector of replacement name(s) to
|
annot_rows |
A character vector of column keys that can be found from
input files of |
xmin |
Numeric; the minimum x at a log2 scale. The default is -1. |
xmax |
Numeric; the maximum x at a log2 scale. The default is 1. |
xmargin |
Numeric; the margin in heat scales. The default is 0.1. |
p_dist_rows |
Numeric; the power of the Minkowski distance in the measures
of row |
p_dist_cols |
Numeric; similar to |
hc_method_rows |
A character string; the same agglomeration method for
|
hc_method_cols |
A character string; similar to |
x |
Dummy argument to avoid incurring the corresponding argument in dist by partial argument matches. |
p |
Dummy argument to avoid incurring the corresponding argument in dist by partial argument matches. |
method |
Dummy argument to avoid incurring the corresponding argument in dist by partial argument matches. |
diag |
Dummy argument to avoid incurring the corresponding argument in dist by partial argument matches. |
upper |
Dummy argument to avoid incurring the corresponding argument in dist by partial argument matches. |
annotation_col |
Dummy argument to avoid incurring the corresponding argument in pheatmap. |
annotation_row |
Dummy argument to avoid incurring the corresponding argument in pheatmap. |
clustering_method |
Dummy argument to avoid incurring the corresponding argument in pheatmap. |
rm_allna |
Logical; if TRUE, removes data rows that are exclusively NA
across ratio columns of |
... |
|
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