Up: Component summary
Up: Component summary
Component
KaplanMeierPlotPlots Kaplan Meier survival plot using the survival and survminer R packages. Optionally forest plot is produced if multivariate Cox model is performed.
| Version | 1.0 |
|---|---|
| Bundle | tools |
| Categories | Analysis |
| Authors | Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | survival (R-package) ; survminer (R-package) ; cowplot (R-package) ; ggthemes (R-package) ; ggplot2 (R-package) ; broom (R-package) |
| Source files | component.xml KaplanMeierPlot.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | CSV | Optional | Input csv file having survival data (time , event, grouping). |
Outputs| Name | Type | Description |
|---|---|---|
| plots | BinaryFolder | Folder containing plots in pdf format. |
| plotObject | BinaryFile | The R plot object. Can be read into R using readRDS function to be further edited if needed |
| survPvalue | CSV | A CSV file containing the p-value obtained from the survival analysis |
| CoxStats | CSV | If run, this output will have the Cox multivariate regression statistics |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| eventText | string | "DEAD" | The text in statusColumn pointing to an event. |
| ggplotExtra | string | "" | ggplot expressions to be added to the plot to allow advanced customization. e.g. "ggtitle('my plot') + theme(plot.title = element_text(size = 20))". |
| groupColumn | string | "group" | Name of the column having the groups to be differentiated. |
| otherOptions | string | "" | A string of function parameters to be pasted in the ggsurvplot call. e.g. "conf.int = T, linetype = 2" |
| showPval | boolean | true | Whether the p-value is printed on the plot. |
| showRiskTable | boolean | true | Whether to show the risk table in the plot. |
| statusColumn | string | "status" | Name of the column having the events. |
| strataCols | string | "" | Comma separated columns name to be dependent variables in Cox multivariate analysis |
| timeColumn | string | "time" | Name of the column having the follow up time. |
| xlabel | string | "Time" | Title of the x axis. |
| ylabel | string | "Survival Probability" | Title of the y axis. |
Test cases| Test case | Parameters▼ | IN in |
OUT plots |
OUT plotObject |
OUT survPvalue |
OUT CoxStats |
|---|---|---|---|---|---|---|
| case1 | properties | in | (missing) | (missing) | (missing) | (missing) |
|
groupColumn=sex, |
||||||
| case2 | properties | in | (missing) | (missing) | (missing) | (missing) |
|
groupColumn=sex, |
||||||