Plot a cycle-specific summary graph of maintenance therapy (MT) data for single patient

Create summary graph with maintenance therapy data. Weighted mean absolute neutrophil count (ANC) and dose information is calculated and plotted for each cycle.

Usage

summarize_cycle_progression(input_file_path, anc_range, unit)

Arguments

input_file_path

Path to input csv file for the patient (in quotes)

anc_range

ANC target range as per the protocol: (c(lower threshold, upper threshold)). NOTE: Ensure that units are the same as unit of ANC in the input data.

unit

Choose either "million" or "billion".

"million" = million cells/L (x\(10^{6}\) cells/L or cells/\(\mu\)l)
"billion" = billion cells/L (x\(10^{9}\) cells/L or x\(10^{3}\) cells/\(\mu\)l)

Value

Plot image

Note

If there is only one threshold for anc_range parameter, please specify the respective value and keep the other threshold as NA. eg : c(2000, NA)
Horizontal dotted lines on the graph indicate anc_range thresholds.Red dot represents summarized overall MT data.

Examples

pat_data = system.file("extdata/processed_data/", "UPN_916.csv", package = "allMT")
summarize_cycle_progression(input_file_path = pat_data, anc_range = c(0.75, 1.5),
                 unit = "billion")
#> NOTE: Analyzing provided input file
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Cycle progression summary graph created
#> Quitting
#> Bye Bye: Did you know that Saturn is second largest planet in our solar system :)?
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Removed 1 rows containing missing values (`geom_rect()`).
#> Warning: Removed 1 rows containing missing values (`geom_vline()`).
#> Warning: Removed 1 rows containing missing values (`geom_point()`).
#> Warning: Removed 1 row containing missing values (`geom_path()`).

# \donttest{
summarize_cycle_progression(input_file_path = pat_data,
                 anc_range = c(0.8, 2), unit = "billion")
#> NOTE: Analyzing provided input file
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Cycle progression summary graph created
#> Quitting
#> Bye Bye: Did you know that Saturn is second largest planet in our solar system :)?
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Removed 1 rows containing missing values (`geom_rect()`).
#> Warning: Removed 1 rows containing missing values (`geom_vline()`).
#> Warning: Removed 1 rows containing missing values (`geom_point()`).
#> Warning: Removed 1 row containing missing values (`geom_path()`).


# As per BFM protocol (Reference PMID - 15902295):
summarize_cycle_progression(input_file_path = pat_data,
                 anc_range = c(2, NA),
                 unit = "billion")
#> NOTE: Analyzing provided input file
#> Error
#> <simpleError in if (anc_range[1] > 100 | anc_range[2] > 100) {    message("Warning: Are you sure the anc_range corresponds to the selected 'unit'?")}: missing value where TRUE/FALSE needed>
#> Quitting
#> Bye Bye: Did you know that Saturn is second largest planet in our solar system :)?

# As per St Jude protocol (Reference PMID - 15902295):
summarize_cycle_progression(input_file_path = pat_data,
                 anc_range = c(0.8, 2),
                 unit = "billion")
#> NOTE: Analyzing provided input file
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.
#> Cycle progression summary graph created
#> Quitting
#> Bye Bye: Did you know that Saturn is second largest planet in our solar system :)?
#> Warning: Using size for a discrete variable is not advised.
#> Warning: Removed 1 rows containing missing values (`geom_rect()`).
#> Warning: Removed 1 rows containing missing values (`geom_vline()`).
#> Warning: Removed 1 rows containing missing values (`geom_point()`).
#> Warning: Removed 1 row containing missing values (`geom_path()`).


# }