complex_heatmap_exposures {YAPSA} | R Documentation |
The PIDs are clustered according to their signature exposures. uses package ComplexHeatmap by Zuguang Gu. This function calls:
complex_heatmap_exposures( in_exposures_df, in_subgroups_df, in_signatures_ind_df, in_data_type = "norm exposures", in_method = "manhattan", in_subgroup_column = "subgroup", in_subgroup_colour_column = NULL, in_palette = colorRamp2(c(0, 0.2, 0.4, 0.6), c("white", "yellow", "orange", "red")), in_cutoff = 0, in_filename = NULL, in_column_anno_borders = FALSE, in_row_anno_borders = FALSE )
in_exposures_df |
Numerical data frame encoding the exposures |
in_subgroups_df |
A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup |
in_signatures_ind_df |
A data frame containing meta information about the signatures, especially the asserted colour |
in_data_type |
Title in the figure |
in_method |
Method of the clustering to be supplied to
|
in_subgroup_column |
Indicates the name of the column in which the
subgroup information is encoded in |
in_subgroup_colour_column |
Indicates the name of the column in which
the colour information for subgroups is encoded in |
in_palette |
Palette with colours for the heatmap. Default is
|
in_cutoff |
A numeric value less than 1. Signatures from within |
in_filename |
A path to save the heatmap. If none is specified, the figure will be plotted to the running environment. |
in_column_anno_borders |
Whether or not to draw separating lines between the fields in the annotation |
in_row_anno_borders |
Whether or not to draw separating lines between the fields in the annotation |
It might be necessary to install the newest version of the
development branch of the packages circlize and ComplexHeatmap by
Zuguang Gu: devtools::install_github("jokergoo/circlize")
and
devtools::install_github("jokergoo/ComplexHeatmap")
The function doesn't return any value.
data(lymphoma_cohort_LCD_results) complex_heatmap_exposures( rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df, COSMIC_subgroups_df, chosen_signatures_indices_df, in_data_type="norm exposures", in_subgroup_colour_column="col", in_method="manhattan", in_subgroup_column="subgroup")