circos_plot: Create a Circos plot with up to 3 tracks
In mattlee821/EpiCircos: An implementation of Circos plots for epidemiologists

Description Usage Arguments Examples

View source: R/circos_plot.R

Create a Circos plot with up to 3 tracks

circos_plot(
  track_number,
  track1_data,
  track2_data,
  track3_data,
  track1_type,
  track2_type,
  track3_type,
  label_column,
  section_column,
  order = TRUE,
  order_column,
  estimate_column,
  pvalue_column,
  pvalue_adjustment,
  lower_ci,
  upper_ci,
  lines_column,
  lines_type = "o",
  bar_column,
  histogram_column,
  histogram_binsize = 0.01,
  histogram_densityplot = FALSE,
  legend = FALSE,
  track1_label = NA,
  track2_label = NA,
  track3_label = NA,
  pvalue_label = NA,
  circle_size = 25,
  track1_height = 0.2,
  track2_height = 0.2,
  track3_height = 0.2
)

`track_number`	The number of tracks you wnat your circos plot to have. Maximum number of tracks is 3.
`track1_data`	The data frame of your first track.
`track2_data`	The data frame of your second track.
`track3_data`	The data frame of your third track.
`track1_type`	The type of plot for the first track. One of "scatter", "lines", "bar" and "histogram".
`track2_type`	The type of plot for the second track. One of "scatter", "lines", "bar" and "histogram".
`track3_type`	The type of plot for the third track. One of "scatter", "lines", "bar" and "histogram".
`label_column`	The column in your data frames that you will use as the labels for the circos plot. This will likely be the column with your exposure/outcome name in. Labels go on the outside of the plot.
`section_column`	The column in your data frames that you will use to group/section your data/plot by.
`order`	Do you want MR Viz to organise your columns alphabetically. Default is TRUE
`order_column`	If order = FALSE what column do you want to order your sections by
`estimate_column`	The column in your data frames with the estimates in.
`pvalue_column`	The column in your data frames with the p-values in.
`pvalue_adjustment`	The threshold you want to set your p-value 'significance' threshold too. This can be in the format of a single value or a function e.g. 0.05/22. The p-value thrshold is only used for scatter plots.
`lower_ci`	The column in your data frames with the lower confidence intervals in.
`upper_ci`	The column in your data frames with the upper confidence intervals in.
`lines_column`	The column in your data frames that you want to plot as lines.
`lines_type`	The type of line plot you want. "l" = straight lines; "o" = straight lines with points; "s" = boxed lines; "h" = vertical lines. Default is "o".
`bar_column`	The column in your data frames that you want to plot as bars.
`histogram_column`	The column in your data frames that you want to plot as histograms.
`histogram_binsize`	The binsize of the histogram. Default is 0.01.
`histogram_densityplot`	Do you want your histogram to be a density plot or not. Default is FALSE.
`legend`	Do you want a legend = TRUE or FALSE. FALSE by default
`track1_label`	What do you want the label for the first track to be e.g. "Body Mass Index"
`track2_label`	What do you want the label for the first track to be e.g. "Corondary Heart Disease"
`track3_label`	What do you want the label for the first track to be e.g. "Breast Cancer"
`pvalue_label`	What do you want the label for the p-value to read e.g. "p-value <= 0.05"
`circle_size`	The size of the circos plot. Smaller numbers make larger circos plots. Default is 25. You will need to adjust this number a few times to get the perfect size for your specific circos plot requirements. If you have long labels then try ≥ 25. If your labels are short try 1-10.
`track1_height`	Size of the track as a percent of the whole circle. Default is 20 percent (0.20)
`track2_height`	Size of the track as a percent of the whole circle. Default is 20 percent (0.20)
`track3_height`	Size of the track as a percent of the whole circle. Default is 20 percent (0.20). It is sometimes worth increasing the size of track 3 to 30 percent

circos_plot(track_number = 3,
track1_data = EpiCircos_data,
track2_data = EpiCircos_data,
track3_data = EpiCircos_data,
track1_type = "points",
track2_type = "lines",
track3_type = "bar",
label_column = 1,
section_column = 2,
estimate_column = 4,
pvalue_column = 5,
pvalue_adjustment = 0.05,
lower_ci = 7,
upper_ci = 8,
lines_column = 4,
lines_type = "o",
bar_column = 4,
histogram_column = 4,
histogram_binsize = 0.01,
histogram_densityplot = F,
legend = FALSE,
circle_size = 25)