diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R index 8609042e15f254b95bd9667b8b99bf401e4bd7be..2b50752875b25d6d3182fd8c29e58fbf6804ada0 100644 --- a/R/shiny-ui-base.R +++ b/R/shiny-ui-base.R @@ -823,7 +823,6 @@ mk_shinyscreen_server <- function(projects,init) { p = make_eic_ms1_plot(db=db, - extr_ms1=ms1, summ, kvals=rf_get_cindex_kval(), labs=rf_get_cindex_labs(), @@ -855,12 +854,13 @@ mk_shinyscreen_server <- function(projects,init) { gg = rf_plot_eic_ms1() rt_rng = range(gg$data$rt) - p = make_eic_ms2_plot(summ, - kvals=rf_get_cindex_kval(), - labs=rf_get_cindex_labs(), - rt_range = rf_get_ms2_eic_rtrange(), - asp=PLOT_EIC_ASPECT, - colrdata=rf_colrdata()) + p = make_eic_ms2_plot(rvs$m$db, + summ, + kvals=rf_get_cindex_kval(), + labs=rf_get_cindex_labs(), + rt_range = rf_get_ms2_eic_rtrange(), + asp=PLOT_EIC_ASPECT, + colrdata=rf_colrdata()) p = if (!is.null(p)) p else empty_plot("Nothing to plot") @@ -886,11 +886,11 @@ mk_shinyscreen_server <- function(projects,init) { }) req(NROW(summ)>0L) req(NROW(ms2)>0L) - p = make_spec_ms2_plot(ms2, - summ, - kvals=req(rf_get_cindex_kval()), - labs=req(rf_get_cindex_labs()), - colrdata=rf_colrdata()) + p = make_spec_ms2_plot(db = rvs$m$db, + summ, + kvals=req(rf_get_cindex_kval()), + labs=req(rf_get_cindex_labs()), + colrdata=rf_colrdata()) p = if (!is.null(p)) p else empty_plot("Nothing to plot") p @@ -1326,7 +1326,6 @@ mk_shinyscreen_server <- function(projects,init) { message('Compound index row: ',ri) p1 = make_eic_ms1_plot(db=db, - ms1, summ, kvals=kvals, labs=labs, @@ -1335,11 +1334,12 @@ mk_shinyscreen_server <- function(projects,init) { i_range=i_range, colrdata = colrdata) + theme_print() - p2 = make_eic_ms2_plot(summ,kvals=kvals, - labs=labs, - asp=PLOT_EIC_ASPECT, - rt_range=rt_range, - colrdata = colrdata) + theme_print() + p2 = make_eic_ms2_plot(db=db, + summ,kvals=kvals, + labs=labs, + asp=PLOT_EIC_ASPECT, + rt_range=rt_range, + colrdata = colrdata) + theme_print() @@ -1347,11 +1347,11 @@ mk_shinyscreen_server <- function(projects,init) { smi = rvs$m$out$tab$comp[ID==(id),SMILES][[1]] p_struc = make_struct_plot(smi) - p_spec = make_spec_ms2_plot(ms2, - summ, - kvals=kvals, - labs=labs, - colrdata=colrdata)+theme_print() + p_spec = make_spec_ms2_plot(db=db, + summ, + kvals=kvals, + labs=labs, + colrdata=colrdata)+theme_print() cmb = combine_plots(p1,p2,p_spec,p_struc) print(cmb)