fm_plot | R Documentation |
fm_plot
is meant to be used in conjunction with
extractFmFe
to create a graph with overlaid fm and fe data
from a simulation or simulations. UNDER CONSTRUCTION.
fm_plot(
fm_dataframe,
mean_type = "arithmetic",
figure_type = "means only",
linear_or_log = "linear",
colorBy_column,
color_labels = NA,
legend_label_color = NA,
color_set = "default",
linetype_column,
linetypes = c("solid", "dashed"),
line_width = NA,
legend_label_linetype = NA,
facet1_column,
facet1_title = NA,
facet2_column,
facet2_title = NA,
facet_ncol = NA,
facet_nrow = NA,
floating_facet_scale = FALSE,
facet_spacing = NA,
time_range = NA,
x_axis_interval = NA,
x_axis_label = NA,
pad_x_axis = TRUE,
pad_y_axis = TRUE,
y_axis_limits_lin = NA,
y_axis_limits_log = NA,
y_axis_interval = NA,
y_axis_label = NA,
hline_position = NA,
hline_style = "red dotted",
vline_position = NA,
vline_style = "red dotted",
graph_labels = TRUE,
graph_title = NA,
graph_title_size = 14,
prettify_compound_names = TRUE,
legend_position = NA,
existing_exp_details = NA,
return_caption = FALSE,
save_graph = NA,
fig_height = 6,
fig_width = 5,
assume_unique = TRUE
)
fm_dataframe |
input data.frame of fm or fe values generated from
running |
mean_type |
plot "arithmetic" (default) or "geometric" mean concentrations or "median" concentrations as the main (thickest or only) line for each data set. If this aggregate measure is not available in the simulator output, you'll receive a warning message and we'll plot one that is available. |
figure_type |
the type of figure to plot.
|
linear_or_log |
the type of graph to be returned. Options:
|
colorBy_column |
(optional) the column in |
color_labels |
optionally specify a character vector for how you'd like
the labels for whatever you choose for |
legend_label_color |
optionally indicate on the legend something
explanatory about what the colors represent. For example, if
|
color_set |
the set of colors to use. Options:
|
linetype_column |
the column in |
linetypes |
the line types to use. Default is "solid" for all lines.
You'll need one line type for each possible value in the column you
specified for |
line_width |
optionally specify how thick to make the lines. Acceptable input is a number; the default is 1 for most lines and 0.8 for some, to give you an idea of where to start. |
legend_label_linetype |
optionally indicate on the legend something
explanatory about what the line types represent. For example, if
|
facet1_column |
optionally break up the graph into small multiples; this
specifies the first of up to two columns to break up the data by, and the
designated column name should be unquoted, e.g., |
facet1_title |
optionally specify a title to describe facet 1. This is
ignored if |
facet2_column |
optionally break up the graph into small multiples; this
specifies the second of up to two columns to break up the data by, and the
designated column name should be unquoted, e.g., |
facet2_title |
optionally specify a title to describe facet 2. This is
ignored if |
facet_ncol |
optionally specify the number of columns of facetted graphs
you would like to have. This only applies when you have specified a column
for |
facet_nrow |
optionally specify the number of rows of facetted graphs
you would like to have. This only applies when you have specified a column
for |
floating_facet_scale |
TRUE, FALSE (default), "x", "y", or "xy" for whether to allow the axes for each facet of a multi-facetted graph to scale freely to best fit whatever data are present. Default is FALSE, which means that all data will be on the same scale for easy comparison. However, this could mean that some graphs have lines that are hard to see, so you can set this to TRUE to allow the axes to shrink or expand according to what data are present for that facet. If this is set to "x", "y", or "xy", then the scale will only float along that axis. Play around with this to see what we mean. Floating axes comes with a trade-off for the looks of the graphs, though: Setting this to TRUE does mean that your x axis won't automatically have pretty breaks that are sensible for times in hours and that you can't specify intervals or limits for either the x or the y axis. If you're a ggplot2 user, here's what's going on under the hood: If you set
|
facet_spacing |
Optionally set the spacing between facets. If left as
NA, a best-guess as to a reasonable amount of space will be used. Units are
"lines", so try, e.g. |
time_range |
time range to display. Options:
|
x_axis_interval |
set the x-axis major tick-mark interval. Acceptable input: any number or leave as NA to accept default values, which are generally reasonable guesses as to aesthetically pleasing and PK-relevant intervals. |
x_axis_label |
optionally supply a character vector or an expression to use for the x axis label |
pad_x_axis |
optionally add a smidge of padding to the x axis (default
is TRUE, which includes some generally reasonable padding). If changed to
FALSE, the y axis will be placed right at the beginning of your time range
and all data will end exactly at the end of the time range
specified. If you want a specific amount of x-axis padding, set this
to a number; the default is |
pad_y_axis |
optionally add a smidge of padding to the y axis (default
is TRUE, which includes some generally reasonable padding). As with
|
y_axis_limits_lin |
Optionally set the Y axis limits for the linear
plot, e.g., |
y_axis_limits_log |
Optionally set the Y axis limits for the semi-log
plot, e.g., |
y_axis_interval |
set the y-axis major tick-mark interval. Acceptable input: any number or leave as NA to accept default values, which are generally reasonable guesses as to aesthetically pleasing intervals. |
y_axis_label |
optionally supply a character vector or an expression to use for the y axis label |
hline_position |
numerical position(s) of any horizontal lines to add to
the graph. The default is NA to have no lines, and good syntax if you
do want lines would be, for example, |
hline_style |
the line color and type to use for any horizontal lines
that you add to the graph with |
vline_position |
numerical position(s) of any vertical lines to add to
the graph. The default is NA to have no lines, and good syntax if you
do want lines would be, for example, |
vline_style |
the line color and type to use for any vertical lines that
you add to the graph with |
graph_labels |
TRUE or FALSE for whether to include labels (A, B, C, etc.) for each of the small graphs. (Not applicable if only outputting linear or only semi-log graphs.) |
graph_title |
optionally specify a title that will be centered across your graph or set of graphs |
graph_title_size |
the font size for the graph title if it's included; default is 14 |
prettify_compound_names |
TRUE (default), FALSE or a character vector:
This is asking whether to make compound names prettier in legend entries
and in any Word output files. This was designed for simulations where the
substrate and any metabolites, perpetrators, or perpetrator metabolites are
among the standard options for the simulator, and leaving
|
legend_position |
Specify where you want the legend to be. Options are "left", "right" (default in most scenarios), "bottom", "top", or "none" if you don't want one at all. |
return_caption |
TRUE or FALSE (default) for whether to return any
caption text to use with the graph. This works best if you supply something
for the argument |
save_graph |
optionally save the output graph by supplying a file name in quotes here, e.g., "My conc time graph.png"or "My conc time graph.docx". The nice thing about saving to Word is that the figure title and caption text will be partly filled in automatically, although you should check that the text makes sense in light of your exact graph. If you leave off ".png" or ".docx", it will be saved as a png file, but if you specify a different graphical file extension, it will be saved as that file format. Acceptable graphical file extensions are "eps", "ps", "jpeg", "jpg", "tiff", "png", "bmp", or "svg". Do not include any slashes, dollar signs, or periods in the file name. Leaving this as NA means the file will not be automatically saved to disk. |
fig_height |
figure height in inches; default is 6 |
fig_width |
figure width in inches; default is 5 |
assume_unique |
TRUE (default) or FALSE for whether to assume that the concentration-time data contain no replicates, which messes things up and will likely cause this function to crash. Why would you want to skip this? Because it can take a LOOOOOOONG time if you have a lot of points. If you're sure your data are unique, set this to TRUE and save a fair amount of processing time to make your graph. If you're not sure what we're talking about here or if you get error messages that aren't terribly clear (which generally means that R wrote them and not your friendly SimcypConsultancy package authors), try setting this to FALSE. |
a ggplot2 graph
# None yet
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.