Description Usage Arguments Value References Examples
View source: R/radial_plotly.R
This function creates an interactive plotly object which maps differential expression onto a polar coordinates.
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 | radial_plotly(
polar,
colours = c("green3", "cyan", "blue", "purple", "red", "gold2"),
non_sig_colour = "grey60",
colour_scale = "discrete",
continuous_shift = 1.33,
label_rows = NULL,
arrow_length = 50,
grid = NULL,
fc_or_zscore = "zscore",
label_size = 14,
colour_code_labels = TRUE,
label_colour = NULL,
grid_colour = "grey80",
axis_colour = "black",
marker_size = 6,
marker_alpha = 0.7,
marker_outline_colour = "white",
marker_outline_width = 0.5,
axis_title_size = 16,
axis_label_size = 10,
axis_ticks = NULL,
axis_angle = 5/6,
plot_height = 700,
plot_width = 700,
...
)
|
polar |
A polar object with the pvalues between groups of interest and
polar coordinates. Created by |
colours |
A vector of colour names or hex triplets for each of the six groups. Default = c("green3", "cyan", "blue", "purple", "red", "gold2"). Colours are assigned in order: group1+, group1+group2+, group2+, group2+group3+, group3+, group1+group3+. |
non_sig_colour |
The colour for non-significant markers (default = "grey60"). |
colour_scale |
whether to use a 'discrete' or 'continuous' colour scale (default = 'discrete'). |
continuous_shift |
The number of radians (between 0 and 6)
to offset the continuous colour scale by. This is calculated by converting
the angle to a hue using |
label_rows |
A vector of row names or numbers to label. |
arrow_length |
The length of label arrows (default = 50). |
grid |
An optional grid object. If NULL this will be calculated using
the default values of |
fc_or_zscore |
Whether to use the z-score or fold change as magnitude. Options are 'zscore' (default) or 'fc'. |
label_size |
Font size of labels/annotations (default = 14) |
colour_code_labels |
Logical whether label annotations should be colour coded. If FALSE label_colour is used. |
label_colour |
HTML colour of annotation labels if not colour coded. |
grid_colour |
The colour of the grid (default="grey80"). |
axis_colour |
The colour of the grid axes and labels (default="black"). |
marker_size |
Size of the markers (default = 6). |
marker_alpha |
Opacity for the markers (default = 0.7). |
marker_outline_colour |
Colour for marker outline (default = white) |
marker_outline_width |
Width for marker outline (default = 0.5) |
axis_title_size |
Font size for axis titles (default = 16) |
axis_label_size |
Font size for axis labels (default = 10) |
axis_ticks |
A numerical vector of radial axis tick breaks. If
NULL this will be calculated using |
axis_angle |
Angle in radians for the radial axis (default = 5/6). |
plot_height |
Plot height in px (default=700). |
plot_width |
Plot width in px (default=700). |
... |
Optional parameters to pass to
|
Returns a plotly plot featuring variables on a tri-axis radial graph
Lewis, Myles J., et al. (2019). Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes. Cell reports, 28:9
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data(example_data)
syn_polar <- polar_coords(sampledata = syn_example_meta,
contrast = "Pathotype",
groups = NULL,
pvalues = syn_example_p,
expression = syn_example_rld,
p_col_suffix = "pvalue",
padj_col_suffix = "padj",
non_sig_name = "Not Significant",
multi_group_prefix = "LRT",
significance_cutoff = 0.01,
fc_cutoff = 0.3)
radial_plotly(polar = syn_polar, label_rows = c("SLAMF6"))
|
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