phen_block
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | phen_block(
pav_obj,
phen_stat_res,
phen_name,
add_gene_info = "p",
p_threshold = 0.01,
adjust_p = T,
only_show_significant = T,
flip = F,
per_colors = c("#1E90FF", "#EE6363"),
na_col = "gray",
cell_border_color = NA,
gene_info_color_list = NULL,
cluster_rows = T,
clustering_distance_rows = "euclidean",
clustering_method_rows = "complete",
row_dend_side = "left",
row_dend_width = grid::unit(5, "mm"),
row_sorted = c(),
show_row_names = F,
row_names_side = "right",
row_names_size = 10,
row_names_rot = 0,
cluster_columns = T,
clustering_distance_columns = "euclidean",
clustering_method_columns = "complete",
column_dend_side = "top",
column_dend_height = grid::unit(5, "mm"),
column_sorted = c(),
show_column_names = F,
column_names_side = "bottom",
column_names_size = 10,
column_names_rot = 90,
anno_param_gene = list(show = T, width = 5, border = FALSE, name_size = NULL,
name_rot = 90, name_side = "bottom"),
legend_side = "right",
legend_title = list(pav = "PAV", type = "gene"),
legend_title_size = NULL,
legend_text_size = NULL,
legend_grid_size = grid::unit(4, "mm")
)
|
pav_obj |
A PAV object. |
phen_stat_res |
The result from |
phen_name |
The name of phenotype used for grouping. |
add_gene_info |
A character vector of 'gene_info' names. The p_value/p_adjusted will also be added to 'gene_info'. |
p_threshold |
The threshold of p_value/p_adjusted. |
adjust_p |
A logical value indicating whether adjust p_value. |
only_show_significant |
A logical value indicating whether only show p_value/p_adjusted that satisfies the condition. |
flip |
A logical value indicating whether flip cartesian coordinates. |
per_colors |
A vector of colors or a color mapping function for absence percentage, pass to |
na_col |
A string of color for NA values. |
cell_border_color |
'NA' or a string of color for the border of cells. |
gene_info_color_list |
A list contains named vector of colors for 'gene_info' annotation. e.g. list(source = c("reference" = "red", "novel" = "blue"), length = c("orange", "red")) |
cluster_rows |
A logical value indicating whether perform clustering on rows. |
clustering_distance_rows |
Method of measuring distance when clustring on rows, pass to |
clustering_method_rows |
Method to perform hierarchical clustering on rows, pass to |
row_dend_side |
The position of the row dendrogram ("left", "right"). |
row_dend_width |
A |
row_sorted |
A vector of sorted row names. It only works when 'cluster_rows = F'. |
show_row_names |
A logical value indicating whether show row names. |
row_names_side |
The position of row names ("left", "right"). |
row_names_size |
The size of row names. |
row_names_rot |
The rotation of row names. |
cluster_columns |
A logical value indicating whether perform clustering on columns. |
clustering_distance_columns |
Method of measuring distance when clustring on columns, pass to |
clustering_method_columns |
Method to perform hierarchical clustering on columns, pass to |
column_dend_side |
The position of the column dendrogram ("top", "bottom"). |
column_dend_height |
A |
column_sorted |
A vector of sorted column names. It only works when 'cluster_columns = F' and 'split_block = F'. |
show_column_names |
A logical value indicating whether show column names. |
column_names_side |
The position of column names ("top", "column"). |
column_names_size |
The size of column names. |
column_names_rot |
The rotation of column names. |
anno_param_gene |
A list contains parameters for the phenotype annotation. These can be any of the following: "show", "width", "border", "name_size", "name_rot" and "name_side". |
legend_side |
The position of legend ("top", "bottom", "right", "left"). |
legend_title |
The text for the legend title. |
legend_title_size |
The size of legend title. |
legend_text_size |
The size of legend item labels. |
legend_grid_size |
A |
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