incucyte | R Documentation |
This tool generates confluency plots over time starting from incucyte data.
incucyte(
metadata,
raw.data,
comparisons = "all",
error = "SEM",
normalization.method = "none",
start.hour = 0,
plot.days = FALSE,
show.error.ribbon = TRUE,
show.error.bars = FALSE,
show.points = TRUE,
show.lines = TRUE,
show.legend = TRUE,
same.y.scale = TRUE,
group.order = NULL,
error.transparency = 0.25,
point.size = 1,
line.type = 1,
line.smooth.span = 0.25,
colors = NULL,
skip.head.lines.in.data = 1
)
metadata |
Path to a table or a data.frame with at least two columns: 'well.ID' and 'group'. The 'well.id' indicates the ID of the wells/columns in the rawData table; the 'group' indicates the name of the group at which each column belongs (wells belonging to the same column will be averaged together). A third column 'color' can be used to indicate the color; notice that each group should have the same color. |
raw.data |
Path to the rawData table or a data.frame. First column must be 'Elapsed' (the time in hours) and the other columns the wells (e.g., A1, A2, B5, B8, ...). |
comparisons |
List of vectors containing the groups to be used in each comparison: one vector per comparison. E.g.: list(c("group_A", "group_B"), c("group_B", "group_C", "group_E")). Default: |
error |
String to indicate the error type. Possible choices: 'SEM', 'SD'. Default: |
normalization.method |
String to indicate the normalization method. Possible choices: "none", "division", "subtraction". Default: |
start.hour |
Number of hours to be excluded from the calculations. Default: |
plot.days |
Logical value to indicate whether to plotted days instead of hours. Default: |
show.error.ribbon |
Logical value to indicate whether to show the error ribbon. Default: |
show.error.bars |
Logical value to indicate whether to show the error bars. Default: |
show.points |
Logical value to indicate whether to show the individual average points at each time point. Default: |
show.lines |
Logical value to indicate whether to show the interpolation line. Default: |
show.legend |
Logical value to indicate whether to show the color legend. Default: |
same.y.scale |
Logical value to indicate whether the y-axis should show the same limit range. Default: |
group.order |
String vector with the specific order to use for the groups indicated in the metadata (factor levels). Default: |
error.transparency |
Number between 0 and 1 indicating the transparency (alpha) to use for the error ribbon. Default: |
point.size |
Number for the point size. Default: |
line.type |
A vector indicating the line type to use for each group (both numeric and string values accepted). Default: |
line.smooth.span |
Numeric value of the 'span' for the smoothing of the interpolation line. Default: |
colors |
A vector indicating the color to use for each group (any R color format is accepted). Default: |
skip.head.lines.in.data |
Number of lines to be skipped at the beginning of the raw.data file. Default: |
The function returns a list containing:
metadata
: table used for the metadata;
raw.data
: tables used as raw.data;
analyzed.data
: data.frame with the analyzed data (means, n, SEM, SD, groups, ...);
normalized.data
: data.frame with the normalized data used for the plotting;
plot.list
: names list of plots, one plot for each group plus 'all' comparison;
multiplot
: a plot with all the plots in the plot.list .
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